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Summary: In response to corneal injury, an activation of corneal epithelial stem cells and their direct progeny the early transit amplifying (eTA) cells to rapidly proliferate is critical for proper re-epithelialization. Thus, it is important to understand how such stem/eTA cell activation is regulated. Angiotensin-converting enzyme 2 (ACE2) is predominantly expressed in the stem/eTA-enriched limbal epithelium but its role in the limbal epithelium was unclear. Single cell RNA sequencing (scRNA-seq) suggested that Ace2 involved the proliferation of the stem/eTA cells. Ace2 was reduced following corneal injury. Such reduction enhanced limbal epithelial proliferation and downregulated LCN2, a negative regulator of proliferation in a variety of tissues, via upregulating TGFA and consequently activating epidermal growth factor receptor (EGFR). Inhibition of EGFR or overexpression of LCN2 reversed the increased proliferation in limbal epithelial cells lacking ACE2. Our findings demonstrate that after corneal injury, ACE2 is downregulated, which activates limbal epithelial cell proliferation via a TGFA/EGFR/LCN2 pathway.

Background: Cyberbullying and nighttime phone use are independently detrimental to sleep and psychological wellbeing, but whether in combination they might be more disruptive remains unknown. Methods: Students aged 7–19 years (N = 53,734) completed a survey measuring sleep duration, nighttime phone use, cyberbullying, and psychological distress. Results: Across stratification variables of gender (F/M) and age group (primary/secondary-school-aged children), bivariate ordered probit regression revealed that being cyberbullied and nighttime phone use were independent predictors of both increased psychological distress and obtaining

Objective The Children’s Hope Scale (CHS) is a widely used six-item instrument for assessing hope in children. The CHS is thought to contain two dimensions—agency thinking (ability to initiate and sustain action towards goals) and pathways thinking (capacity to find a means to carry out goals)—but there is debate whether the scale is unidimensional rather than bidimensional and the factor structure has yet to be established in Australian children.Method N = 171,052 Australian students (8–18 years of age; 0.3% gender diverse, 48.4% male and 51.3% females) completed the CHS as part of a larger survey examining resilience. Exploratory and confirmatory factor analyses were conducted, and internal consistency was assessed with Cronbach’s alpha.Results Bifactor modelling indicated a single-factor structure for the CHS, and the scale demonstrated good internal consistency (Cronbach’s α = .86) and was sensitive to age and gender differences.Conclusions Our results suggest that the CHS is unidimensional and supports its use for the measurement of hope in children and adolescents aged 8–18 years of age.

BackgroundImmune checkpoint therapies have led to significant breakthroughs in cancer patient treatment in recent years. However, their efficiency is variable, and resistance to immunotherapies is common. VISTA is an immune-suppressive checkpoint inhibitor of T cell response belonging to the B7 family and a promising novel therapeutic target. VISTA is expressed in the immuno-suppressive tumor microenvironment, primarily by myeloid lineage cells, and its genetic knockout or antibody blockade restores an efficient antitumor immune response.MethodsFully human monoclonal antibodies directed against VISTA were produced after immunizing humanized Trianni mice and sorting and sequencing natively-linked B cell scFv repertoires. Anti-VISTA antibodies were evaluated for specificity, cross-reactivity, monocyte and T cell activation, Fc-effector functions, and antitumor efficacy using in vitro and in vivo models to select the KVA12123 antibody lead candidate. The pharmacokinetics and safety profiles of KVA12123 were evaluated in cynomolgus monkeys.ResultsHere, we report the development of a clinical candidate anti-VISTA monoclonal antibody, KVA12123. KVA12123 showed high affinity binding to VISTA through a unique epitope distinct from other clinical-stage anti-VISTA monoclonal antibodies. This clinical candidate demonstrated high specificity against VISTA with no cross-reactivity detected against other members of the B7 family. KVA12123 blocked VISTA binding to its binding partners. KVA12123 induced T cell activation and demonstrated NK-mediated monocyte activation. KVA12123 treatment mediated strong single-agent antitumor activity in several syngeneic tumor models and showed enhanced efficacy in combination with anti-PD-1 treatment. This clinical candidate was engineered to improve its pharmacokinetic characteristics and reduce Fc-effector functions. It was well-tolerated in preclinical toxicology studies in cynomolgus monkeys, where hematology, clinical chemistry evaluations, and clinical observations revealed no indicators of toxicity. No cytokines associated with cytokine release syndrome were elevated.ConclusionThese results establish that KVA12123 is a promising drug candidate with a distinct but complementary mechanism of action of the first generation of immune checkpoint inhibitors. This antibody is currently evaluated alone and in combination with pembrolizumab in a Phase 1/2 open-label clinical trial in patients with advanced solid tumors.

Background: Psychological distress is prevalent amongst hospital in-patient and may predispose patients to potentially preventable readmissions after discharge. A particularly vulnerable group are patients with cardiac disorders. This study tested the feasibility of a brief cognitive behavioural therapy consisting of an in-hospital coping session and a post-discharge healthy sleep session. Methods: Standardised questionnaire were used to assess sleep, coping/distress and wellbeing at baseline (pre-intervention) and one-month post-discharge (post-intervention). Treatment fidelity and acceptability were assessed at follow-up. Participants included 72 inpatients admitted with a cardiac disorder or reported to have a cardiac problem whilst in hospital from a single Australian public hospital. Results: Most (83 %) participants found the intervention helpful/very helpful. At baseline prior to admission, almost half of participants (46 %) reported poor wellbeing, 19 % high levels of distress and poor coping, and 47 % sleeping less than 7 h per night. Following the intervention, 45 % of participants with poor wellbeing at baseline had reliable change in wellbeing at follow-up. Conversely, only 22 % of patients with high levels of coping/distress at baseline demonstrated improved coping/distress at follow-up suggesting smaller gains. On average a large 43 min gain in sleep duration was observed post-treatment in patients with poor sleep at baseline. Fourteen percent of participants were readmitted to hospital within 34-days of discharge. Conclusions: The coping and sleep intervention was well received with positive outcomes in patients especially those reporting high levels of distress for sleep and to lesser extent coping and wellbeing. Future studies to assess the efficacy of the brief intervention at reducing hospital readmissions are needed.

The particular relevance of family in human life and experience, which is addressed in family novels, is also evident in sociological studies. In what way can these views complement each other? The text is meant as a contribution to discuss this question, starting by presenting some statistical data on the contemporary diversity of individual and collective family behaviors. They are summarized in five theses focusing on an elaborated, open understanding of human generativity, i.e. the individual and the institutional shaping of generational relationships. These generalizations allow to build a bridge to studies on the family novel. I postulate that the commonalities of family sociology and family novel can be seen in the critical dealing with notions of normality, the tense shaping of social relationships, and – consequentially – the dynamic search for personal and collective identities. These processes go hand in hand with experiences of ambivalence and practices to cope with them.

IntroductionEmerging infectious diseases are increasingly recognized as a global threat to wildlife. Pandemics in amphibians, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have resulted in biodiversity loss at a global scale. Genomic data suggest a complex evolutionary history of Bd lineages that vary in pathogenicity. Africa harbors a significant proportion of global amphibian biodiversity, and multiple Bd lineages are known to occur there; yet, despite the decline of many host species, there are currently no described Bd-epizootics. Here, we describe the historical and recent biogeographical spread of Bd and assess its risk to amphibians across the continent of Africa.MethodsWe provide a 165-year view of host-pathogen interactions by (i) employing a Bd assay to test 4,623 specimens (collected 1908–2013); (ii) compiling 12,297 published Bd records (collected 1852–2017); (iii) comparing the frequency of Bd-infected amphibians through time by both country and region; (iv) genotyping Bd lineages; (v) histologically identifying evidence of chytridiomycosis, and (vi) using a habitat suitability model to assess future Bd risk.ResultsWe found a pattern of Bd emergence beginning largely at the turn of the century. From 1852–1999, we found low Bd prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and multiple Bd lineages that may be responsible for emergence in different regions. We found that Bd risk to amphibians was highest in much of eastern, central, and western Africa.DiscussionOur study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.

The chemical modification of aeroallergens by reactive oxygen and nitrogen species (ROS/RNS) may contribute to the growing prevalence of respiratory allergies in industrialized countries. Post-translational modifications can alter the immunological properties of proteins, but the underlying mechanisms and effects are not well understood. In this study, we investigate the Toll-like receptor 4 (TLR4) activation of the major birch and grass pollen allergens Bet v 1 and Phl p 5, and how the physiological oxidant peroxynitrite (ONOO–) changes the TLR4 activation through protein nitration and the formation of protein dimers and higher oligomers. Of the two allergens, Bet v 1 exhibited no TLR4 activation, but we found TLR4 activation of Phl p 5, which increased after modification with ONOO– and may play a role in the sensitization against this grass pollen allergen. We attribute the TLR4 activation mainly to the two-domain structure of Phl p 5 which may promote TLR4 dimerization and activation. The enhanced TLR4 signaling of the modified allergen indicates that the ONOO–-induced modifications affect relevant protein-receptor interactions. This may lead to increased sensitization to the grass pollen allergen and thus contribute to the increasing prevalence of allergies in the Anthropocene, the present era of globally pervasive anthropogenic influence on the environment.

The current study investigated the association between psychological factors and financial behaviour during the COVID-19 pandemic in older people. Older people were chosen compared to other age groups because of the relatively greater impact in this age group of suboptimal financial decisions on future financial wellbeing. We hypothesised that the psychological factors facilitating general wellbeing during the COVID-I9 pandemic, i.e., positive mental wellbeing, hope, and positive coping, will have positive effects on financial behaviour. Based on telephone interviews, 1501 older Australians (Men = 750 and Women = 751; 55-64y = 630; > 65y = 871) completed an omnibus questionnaire examining coping, hope, mental wellbeing, and financial behaviour. Data was analysed using logistic regression and an ordinary and two-stage least square frameworks. Analyses revealed that the psychological factors identified as facilitating general wellbeing during the COVID-I9 pandemic also facilitated positive financial behaviour with hope and mental wellbeing emerging as significant determinants. Based on weightings from principal component analysis, one item each from the hope and mental wellbeing scale with eigenvalues > 1 were found to be robust predictors of positive financial behaviours. In conclusion, the findings support the assumption that the psychological factors associated with general wellbeing during the COVID-19 pandemic are also associated with positive financial behaviour. They further raise the possibility that single hope and positive mental well-being items can also be used to monitor psychological health and predict financial behaviour in older people and, in particular, at times of crisis. The latter may be useful measures for government to monitor psychological and financial wellbeing and inform policy for supporting older people at times of crisis.

Purpose: Disruptive airline passenger behaviour (DAPB), i.e. “air rage”, has an adverse impact on crew and passenger well-being and is costly to manage and prevent. Given recent changes in airport management, aircraft design, air traffic volume and behavioural norms this review summaries research findings 1985-2020. Methodology: A systematic review of the research literature containing qualitative or quantitative data examining DAPB. Findings: Nineteen articles satisfied the criteria for inclusion. Most studies involved surveys of cabin crew members and to a lesser extent pilots, airline representatives, passengers and business customers. Content primarily focussed on the frequency and characteristics of DAPB, whilst consequences for staff and evaluation of training to manage DAPB was less represented. A paucity of current research was noted which is not in keeping with the changes over the last decade in the aviation industry and the increase in DAPB events. Originality: This study presents a summary of current findings on DAPB. Practical Implications: A better understanding of the environmental, social and psychological factors underlying DAPB and the effectiveness of staff training and interventions that promote a safe travel environment are required. Social Implications: The current industry trend toward sustainability and better management of security challenges must extend its focus to DAPB, in order to reverse the recent trend of social irresponsibility in air travellers.

This paper explores practices and policies for managing information communication technologies (ICTs) and ensuring healthy and productive work environments in higher education settings. This was informed by: (1) semi-structured interviews with 12 senior Human Resource and Wellbeing personnel recruited from 11 public Australian universities; and (2) a review of policy documents that address ICTs/digital communication sourced from 37 Australian public universities. Analyses revealed that ICT management involved balancing flexibility and boundaries and expectations around responsiveness. Findings from interview data revealed that to improve ICT management it is important to develop university guidance material, detangle the notion of responsibility, establish boundaries around expectations of responsivity, provide more education and develop positive working practices. Thematic analysis and subsequent quantification of 654 policy documents revealed gaps in the university policy context on the topic of digital communication. The largest proportion of policies focused on privacy and security, followed by media representation of the university (e.g., throughout branding), then bullying, harassment and discrimination. We make recommendations for policy and practice improvement. It would be beneficial for future research to assess the impact of enacted digital communication management strategies (e.g., policy interventions) on worker wellbeing and work practice outcomes.

Objective This study investigated the reliability and factor structure of the General Health Questionnaire‐12 (GHQ‐12) in children and adolescents and examined whether the GHQ‐12 is sensitive to expected mental well‐being differences across age and sex. Method Here, N = 180,700 Australian students (7–19 years of age) completed the GHQ‐12 as part of a larger survey, the Resilience Survey (Resilient Youth Australia Limited). Exploratory factor analysis (EFA) was conducted, and internal consistency was assessed with Cronbach's alpha. Linear mixed model ANOVAs were conducted to investigate differences in GHQ‐12 scores between females and males. Results EFA revealed a two‐factor model which was consistent across all age bands—Factor A: General Dysphoria (depression and anxiety), and Factor B: General Functioning (ability to cope with day‐to‐day activities). Internal consistency was good (Cronbach's α > 0.7) in all age bands for total GHQ‐12 and factor scores. Confirmatory factor analysis with a two‐factor correlated structure supported EFA results. Bifactor modelling suggested a unidimensional structure. Males aged 7–9 years had significantly higher (more problematic) total GHQ‐12 scores, General Dysphoria scores and General Functioning scores than females (p < 0.001), and females aged 12–19 years had significantly higher scores than males (p < 0.001). Conclusions Our results support the use of the GHQ‐12 for the measurement of mental well‐being symptoms in children from 7 to 19 years of age. Overall, psychometric properties including sensitivity, suggest that the GHQ‐12 provides a robust indicator of short‐term mental state in children and adolescents.

Environmental pollutants like fine particulate matter can cause adverse health effects through oxidative stress and inflammation. Reactive oxygen and nitrogen species (ROS/RNS) such as peroxynitrite can chemically modify proteins, but the effects of such modifications on the immune system and human health are not well understood. In the course of inflammatory processes, the Toll-like receptor 4 (TLR4) can sense damage-associated molecular patterns (DAMPs). Here, we investigate how the TLR4 response and pro-inflammatory potential of the proteinous DAMPs α-Synuclein (α-Syn), heat shock protein 60 (HSP60), and high-mobility-group box 1 protein (HMGB1), which are relevant in neurodegenerative and cardiovascular diseases, changes upon chemical modification with peroxynitrite.For the peroxynitrite-modified proteins, we found a strongly enhanced activation of TLR4 and the pro-inflammatory transcription factor NF-κB in stable reporter cell lines as well as increased mRNA expression and secretion of the pro-inflammatory cytokines TNF-α, IL-1β, and IL-8 in human monocytes (THP-1). This enhanced activation of innate immunity via TLR4 is mediated by covalent chemical modifications of the studied DAMPs.Our results show that proteinous DAMPs modified by peroxynitrite more potently amplify inflammation via TLR4 activation than the native DAMPs, and provide first evidence that such modifications can directly enhance innate immune responses via a defined receptor. These findings suggest that environmental pollutants and related ROS/RNS may play a role in promoting acute and chronic inflammatory disorders by structurally modifying the body's own DAMPs. This may have important consequences for chronic neurodegenerative, cardiovascular or gastrointestinal diseases that are prevalent in modern societies, and calls for action, to improve air quality and climate in the Anthropocene.

Introduction: Cardiac function is modulated by multiple factors including exogenous (circadian rhythm) and endogenous (ultradian 90–110 min sleep cycle) factors. By evaluating heart rate variability (HRV) during sleep, we will better understand their influence on cardiac activity. The aim of this study was to evaluate HRV in the dark phase of the circadian rhythm during sleep in healthy children and adolescents.Methods: One 3 min segment of pre-sleep electrocardiography (EEG) and 3, 6 min segments of electrocardiography recorded during polysomnography from 75 healthy children and adolescents were sampled during progressive cycles of slow wave sleep (SWS1, SWS2, SWS3). Three, 3 min segments of rapid eye movement sleep (REM) were also assessed, with REM1 marked at the last REM period before awakening. Studies that recorded REM3 prior to SWS3 were used for assessment. HRV variables include the following time domain values: mean NN (average RR intervals over given time), SDNN (Standard Deviation of RR intervals), and RMSSD (root Mean Square of beat-to-beat Differences). Frequency domain values include: low frequency (LF), high frequency (HF), and LF:HF.Results: Mixed linear effects model analysis revealed a significant difference in time and frequency domain values between sleep cycles and stages. Mean NN was lowest (highest heart rate) during pre—sleep then significantly increased across SWS1-3. Mean NN in SWS1 was similar to all REM periods which was significantly lower than both SWS2 and SWS3. SDNN remained at pre-sleep levels until SWS3, and then significantly increased in REM1&2. There was a large drop in LF from pre-sleep to SWS1. As cycles progressed through the night, LF remains lower than awake but increases to awake like levels by REM2. RMSSD and HF were lowest in pre-sleep and increased significantly by SWS1 and remain high and stable across stages and cycles except during the REM3 period where RMSSD decreased.Conclusion: Our results demonstrate that there are considerable changes in the spectral analysis of cardiac function occurring during different sleep stages and between sleep cycles across the night. Hence, time of night and sleep stage need to be considered when reporting any HRV differences.

Hydrogen, as a medical gas, is a promising emerging treatment for many diseases related to inflammation and oxidative stress. Molecular hydrogen can be generated through hydrogen ion reduction by a metal, and magnesium-containing effervescent tablets constitute an attractive formulation strategy for oral delivery. In this regard, saccharide-based excipients represent an important class of potential fillers with high water solubility and sweet taste. In this study, we investigated the effect of different saccharides on the morphological and mechanical properties and the disintegration of hydrogen-generating effervescent tablets prepared by dry granulation. Mannitol was found to be superior to other investigated saccharides and promoted far more rapid hydrogen generation combined with acceptable mechanical properties. In further product optimization involving investigation of lubricant effects, adipic acid was selected for the optimized tablet, due to regulatory considerations.

Objective: Microhabitats in the oral cavity differ in microbial taxonomy. However, abundance variations of bacterial and viral communities within these microhabitats are not fully understood. Aims and Hypothesis: To assess the spatial distribution and dynamics of the microbial abundances within 6 microhabitats of the oral cavity before and after sleep. We hypothesise that the abundance distributions of these microbial communities will differ among oral sites. Methods: Using flow cytometry, bacterial and virus-like particle (VLP) abundances were enumerated for 6 oral microhabitats before and after sleep in 10 healthy paediatric sleepers. Results: Bacterial counts ranged from 7.2 ± 2.8 × 105 at the palate before sleep to 1.3 ± 0.2 × 108 at the back of the tongue after sleep, a difference of 187 times. VLPs ranged from 1.9 ± 1.0 × 106 at the palate before sleep to 9.2 ± 5.0 × 107 at the back of the tongue after sleep, a difference of 48 times. Conclusion: The oral cavity is a dynamic numerically heterogeneous environment where microbial communities can increase by a count of 100 million during sleep. Quantification of the paediatric oral microbiome complements taxonomic diversity information to show how biomass varies and shifts in space and time.

Amylase trypsin inhibitors (ATI) can be found in all gluten containing cereals and are, therefore, ingredient of basic foods like bread or pasta. In the gut ATI can mediate innate immunity via activation of the Toll-like receptor 4 (TLR4) on immune cells residing in the lamina propria, promoting intestinal, as well as extra-intestinal, inflammation. Inflammatory conditions can induce formation of peroxynitrite (ONOO−) and, thereby, endogenous protein nitration in the body. Moreover, air pollutants like ozone (O3) and nitrogen dioxide (NO2) can cause exogenous protein nitration in the environment. Both reaction pathways may lead to the nitration of ATI. To investigate if and how nitration modulates the immunostimulatory properties of ATI, they were chemically modified by three different methods simulating endogenous and exogenous protein nitration and tested in vitro. Here we show that ATI nitration was achieved by all three methods and lead to increased immune reactions. We found that ATI nitrated by tetranitromethane (TNM) or ONOO− lead to a significantly enhanced TLR4 activation. Furthermore, in human primary immune cells, TNM nitrated ATI induced a significantly higher T cell proliferation and release of Th1 and Th2 cytokines compared to unmodified ATI. Our findings implicate a causative chain between nitration, enhanced TLR4 stimulation, and adaptive immune responses, providing major implications for public health, as nitrated ATI may strongly promote inhalative wheat allergies (baker's asthma), non-celiac wheat sensitivity (NCWS), other allergies, and autoimmune diseases. This underlines the importance of future work analyzing the relationship between endo- and exogenous protein nitration, and the rise in incidence of ATI-related and other food hypersensitivities.

OBJECTIVES: The aim of this review was to identify which limited wake shift work schedules (LWSW) best promote sleep, alertness, and performance. LWSW are fixed work/rest cycles where the time-at-work does is ≤8 hours and there is >1 rest period per day, on average, for ≥2 consecutive days. These schedules are commonly used in safety-critical industries such as transport and maritime industries. METHODS: Literature was sourced using PubMed, Embase, PsycInfo, Scopus, and Google Scholar databases. We identified 20 independent studies (plus a further 2 overlapping studies), including 5 laboratory and 17 field-based studies focused on maritime watch keepers, ship bridge officers, and long-haul train drivers. The measurement of outcome measures was varied, incorporating subjective and objective measures of sleep: sleep diaries (N=5), actigraphy (N=4), and polysomnography, (N=3); sleepiness: Karolinska Sleepiness Scale (N=5), visual analog scale (VAS) alertness (N=2) and author-derived measures (N=2); and performance: Psychomotor Vigilance Test (PVT) (N=5), Reaction Time or Vigilance tasks (N=4), Vector and Letter Cancellation Test (N=1), and subjective performance (N=2). RESULTS: Of the three primary rosters examined (6 hours-on/6 hours-off, 8 hours-on/8 hours-off and 4 hours-on/8 hours-off), the 4 hours-on/8 hours-off roster was associated with better sleep and lower levels of sleepiness. Individuals working 4 hours-on/8 hours-off rosters averaged 1 hour more sleep per night than those working 6 hours-on/6 hours-off and 1.3 hours more sleep than those working 8 hours-on/8 hours-off (P

Herbal extracts represent an ample source of natural compounds, with potential to be used in improving human health. There is a growing interest in using natural extracts as possible new treatment strategies for inflammatory diseases. We therefore aimed at identifying herbal extracts that affect inflammatory signaling pathways through toll-like receptors (TLRs), TLR2 and TLR4. Ninety-nine ethanolic extracts were screened in THP-1 monocytes and HeLa-TLR4 transfected reporter cells for their effects on stimulated TLR2 and TLR4 signaling pathways. The 28 identified anti-inflammatory extracts were tested in comparative assays of stimulated HEK-TLR2 and HEK-TLR4 transfected reporter cells to differentiate between direct TLR4 antagonistic effects and interference with downstream signaling cascades. Furthermore, the ten most effective anti-inflammatory extracts were tested on their ability to inhibit nuclear factor-κB (NF-κB) translocation in HeLa-TLR4 transfected reporter cell lines and for their ability to repolarize M1-type macrophages. Ethanolic extracts which showed the highest anti-inflammatory potential, up to a complete inhibition of pro-inflammatory cytokine production were Castanea sativa leaves, Cinchona pubescens bark, Cinnamomum verum bark, Salix alba bark, Rheum palmatum root, Alchemilla vulgaris plant, Humulus lupulus cones, Vaccinium myrtillus berries, Curcuma longa root and Arctostaphylos uva-ursi leaves. Moreover, all tested extracts mitigated not only TLR4, but also TLR2 signaling pathways. Seven of them additionally inhibited translocation of NF-κB into the nucleus. Two of the extracts showed impact on repolarization of pro-inflammatory M1-type to anti-inflammatory M2-type macrophages. Several promising anti-inflammatory herbal extracts were identified in this study, including extracts with previously unknown influence on key TLR signaling pathways and macrophage repolarization, serving as a basis for novel lead compound identification.

BackgroundSleep disordered breathing in children is associated with increased blood flow velocity and sympathetic overactivity. Sympathetic overactivity results in peripheral vasoconstriction and reduced systemic vascular compliance, which increases blood flow velocity during systole. Augmented blood flow velocity is recognized to promote vascular remodeling. Importantly, increased vascular sympathetic nerve fiber density and innervation in early life plays a key role in the development of early‐onset hypertension in animal models. Examination of sympathetic nerve fiber density of the tonsillar arteries in children undergoing adenotonsillectomy for Sleep disordered breathing will address this question in humans. Methods and ResultsThirteen children scheduled for adenotonsillectomy to treat sleep disordered breathing underwent pupillometry, polysomnography, flow‐mediated dilation, resting brachial artery blood flow velocity (velocity time integral), and platelet aggregation. The dorsal lingual artery (tonsil) was stained and immunofluorescence techniques used to determine sympathetic nerve fiber density. Sympathetic nerve fiber density was correlated with increased resting velocity time integral (r=0.63; P

BACKGROUND: The Canadian Association for the Study of the Liver, and The Association of Medical Microbiology and Infectious Diseases Canada, jointly developed the Canadian Chronic Hepatitis B (HBV) Consensus Guidelines to assist practitioners involved in the management of this complex disease. These guidelines were published in The Canadian Journal of Gastroenterology in June 2007 and distributed to all Canadian gastroenterologists and hepatologists.

BACKGROUND: The test-retest reliability of temporal summation (TS) and diffuse noxious inhibitory control (DNIC) has not been reported to date. Establishing such reliability would support the possibility of future experimental studies examining factors affecting TS and DNIC. Similarly, the use of manual algometry to induce TS, or an occlusion cuff to induce DNIC of TS to mechanical stimuli, has not been reported to date. Such devices may offer a simpler method than current techniques for inducing TS and DNIC, affording assessment at more anatomical locations and in more varied research settings.

BACKGROUND:Sleep Disordered Breathing (SDB) is a common childhood disorder that encompasses a range of sleep-related upper airway obstruction. Children with SDB demonstrate significant neurocognitive deficits. Adenotonsillectomy is the first line of treatment for SDB and whilst this improves respiratory disturbance, it remains to be established whether neurocognitive gains also result. METHODS:A total of 44 healthy snoring children aged 3-12 years awaiting adenotonsillectomy (SDB group), and 48 age and gender matched non-snoring controls from the general community, completed the study. All children underwent polysomnography and neurocognitive assessment at baseline and after a 6-month follow-up (after surgery in the snoring group). Our primary aim was to determine whether neurocognitive deficits in snoring children were significantly improved following adenotonsillectomy. RESULTS:Wide ranging neurocognitive deficits were found at baseline in SDB children compared to controls, most notably a 10 point IQ difference (P

We introduce a new basis for the algebra of quasisymmetric functions that naturally partitions Schur functions, called quasisymmetric Schur functions. We describe their expansion in terms of fundamental quasisymmetric functions and determine when a quasisymmetric Schur function is equal to a fundamental quasisymmetric function. We conclude by describing a Pieri rule for quasisymmetric Schur functions that naturally generalizes the Pieri rule for Schur functions.

Im vorliegenden Beitrag wird untersucht, welche Bedeutung einer neuen Partnerschaft nach einer Scheidung im mittleren Lebensalter für die Reorganisation der Familie zugeschrieben wird und welche Zusammenhänge dabei zur Art der Beziehungen zwischen geschiedenen Eltern und ihren erwachsenen Kindern bestehen. Auf der Grundlage von 54 ausführlichen Interviews und mittels inhaltsanalytischer Verfahren konnten vier Muster der Verknüpfung der Bedeutung einer neuen Partnerschaft mit der Gestaltung und dem Verständnis von Generationenbeziehungen nachgewiesen werden. Es zeigte sich, daß nicht der Sachverhalt einer neuen oder fehlenden neuen Partnerschaft für sich allein für die Generationenbeziehungen von Belang ist, sondern vielmehr, ob und in welcher Weise er sich mit dem allgemeinen Familienbild einerseits und mit den subjektiven Familienerfahrungen andererseits verbindet. Dies kann als soziale Beziehungslogik verstanden werden, die sich in zwei unterschiedlichen Handlungsstrategien, umschreibbar als Reproduktion und Reform, ausdrückt und das jeweilige Verhalten den Umständen entsprechend steuert.

Wenn der Familienrhetorik eine konstitutive Rolle bei der Herausbildung subjektiver Orientierungen sowie öffentlicher und privater Perspektiven bezüglich Familie eingeräumt wird, dann kann die Herausarbeitung und Identifizierung verbreiteter und wirksamer rhetorischer Elemente auch viel über das konkrete Erleben und das von ihm bestimmte Handeln in der gesellschaftlichen Praxis aussagen. Wissenschaftstheoretisch gesprochen wird hier für eine konstruktiv-pragmatische Orientierung plädiert, in der der Anspruch heruntergeschraubt wird, die 'wahren' Sachverhalte hinter oder unter den subjektiven, privaten und institutionellen Repräsentationen könnten wissenschaftlich zutage gefördert und dementsprechend 'entlarvt' werden.

Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here we develop well-controlled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent standard datasets and published datasets, we benchmark the performance of Scout and existing XL-MS software. We find that Scout offers an excellent combination of speed, sensitivity and false discovery rate control. The results illustrate how our large recombinant standard can support the development of XL-MS analysis tools and evaluation of XL-MS results., Competing Interests: Competing interests: F.L. is a shareholder and advisory board member of Absea Biotechnology Ltd and VantAI. T.C. is the co-founder of Absea Biotechnology Ltd. S.W. is an employee of Absea Biotechnology Ltd. The remaining authors declare no competing interests., (© 2024. The Author(s).)

This data descriptor presents a curated dataset for pathogen detection and identification (Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans) directly from whole-blood samples. The dataset was created using differential cell lysis combined with rapid extraction, digestion, and mass spectrometry-based proteomics. Our method offers a rapid diagnostic alternative to traditional culture, enabling timely disease management, such as sepsis. Highlighting our dataset's uniqueness, it features a three-tier structure: Spectral Libraries of Pathogens for identifying peptide peaks for putative biomarkers; Spiked pathogen in blood MS data for biomarker panel optimization through varied concentration samples; and Parallel Reaction Monitoring (PRM) data from sepsis patients for validating our biomarker panel, achieving 83.3% sensitivity within seven hours without microbial enrichment culture. This dataset serves as a comprehensive reference for bioinformatic tool development and biomarker panel proposals, advancing microbial detection, antimicrobial resistance, and epidemiological studies., (© 2024. The Author(s).)

We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 introduces four main modules, each providing distinct and new functionalities: 1) Pair Finder, which identifies ion doublets characteristic of cleavable cross-linking experiments; 2) Diagnostic Peak Finder, which locates potential reporter ions associated with a specific cross-linker; 3) Precursor Signal Ratio, which computes the ratio between precursor intensity and the total signal in an MS/MS scan; and 4) Xrea, which evaluates spectral quality by analyzing the heterogeneity of peak intensities within a spectrum. These modules collectively streamline the process of optimizing mass spectrometry data acquisition for both Proteomics and XL-MS experiments. RawVegetable 2.0, along with a comprehensive tutorial is freely accessible for academic use at: http://patternlabforproteomics.org/rawvegetable2.

This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab. Further open-search attempts via FragPipe yielded an additional ∼20% identifications, suggesting the remaining unidentified spectra likely arise from complex combinations of post-translational modifications and amino-acid substitutions. This highlights the untapped potential of the dataset for future discoveries, particularly given the importance of PTMs, which remain elusive to nucleotide sequencing approaches but are crucial for understanding biological mechanisms. Our innovative approach extends beyond the identifications that are typically subjected to the bias of a search engine; we discern which spectral clusters are differential and subject them to increased scrutiny, akin to spectral library matching by comparing captured spectra to themselves. Our analysis reveals adaptations in the resistant strain, including enhanced detoxification, altered protein synthesis, and metabolic adjustments. SIGNIFICANCE: We present comprehensive proteomic profiles of non-resistant and resistant Acinetobacter baumannii from Brazilian Hospitals strains, and highlight the presence of discriminative and yet unidentified mass spectral clusters. Our work emphasizes the importance of exploring this overlooked data, as it could hold the key to understanding the complex dynamics of antibiotic resistance. This approach not only informs antimicrobial stewardship efforts but also paves the way for the development of innovative diagnostic tools. Thus, our findings have profound implications for the field, as far as methods for providing a new perspective on diagnosing antibiotic resistance as well as classifying proteomes in general., Competing Interests: Declaration of Competing Interest The authors declare to have no conflict of interests., (Copyright © 2023. Published by Elsevier B.V.)

Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding at best in identifying only one of the multiple cofragmenting peptides. We present PatternLab V (PLV), an updated version of PatternLab that integrates the YADA 3 deconvolution algorithm to handle such cases efficiently. In general, we expect an increase of 10% in spectral identifications when dealing with complex proteomic samples. PLV is freely available at http://patternlabforproteomics.org.

Motivation: Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra., Results: In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm., Availability and Implementation: Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3., Supplementary Information: Supplementary information is available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Shotgun proteomics aims to identify and quantify the thousands of proteins in complex mixtures such as cell and tissue lysates and biological fluids. This approach uses liquid chromatography coupled with tandem mass spectrometry and typically generates hundreds of thousands of mass spectra that require specialized computational environments for data analysis. PatternLab for proteomics is a unified computational environment for analyzing shotgun proteomic data. PatternLab V (PLV) is the most comprehensive and crucial update so far, the result of intensive interaction with the proteomics community over several years. All PLV modules have been optimized and its graphical user interface has been completely updated for improved user experience. Major improvements were made to all aspects of the software, ranging from boosting the number of protein identifications to faster extraction of ion chromatograms. PLV provides modules for preparing sequence databases, protein identification, statistical filtering and in-depth result browsing for both labeled and label-free quantitation. The PepExplorer module can even pinpoint de novo sequenced peptides not already present in the database. PLV is of broad applicability and therefore suitable for challenging experimental setups, such as time-course experiments and data handling from unsequenced organisms. PLV interfaces with widely adopted software and community initiatives, e.g., Comet, Skyline, PEAKS and PRIDE. It is freely available at http://www.patternlabforproteomics.org ., (© 2022. Springer Nature Limited.)

Metacaspases are known to have a fundamental role in apoptosis-like, a programmed cellular death (PCD) in plants, fungi, and protozoans. The last includes several parasites that cause diseases of great interest to public health, mostly without adequate treatment and included in the neglected tropical diseases category. One of them is Trypanosoma cruzi which causes Chagas disease and has two metacaspases involved in its PCD: TcMCA3 and TcMCA5. Their roles seemed different in PCD, TcMCA5 appears as a proapoptotic protein negatively regulated by its C-terminal sequence, while TcMCA3 is described as a cell cycle regulator. Despite this, the precise role of TcMCA3 and TcMCA5 and their atomic structures remain elusive. Therefore, developing methodologies to allow investigations of those metacaspases is relevant. Herein, we produced full-length and truncated versions of TcMCA5 and applied different strategies for their folded recombinant production from E. coli inclusion bodies. Biophysical assays probed the efficacy of the production method in providing a high yield of folded recombinant TcMCA5. Moreover, we modeled the TcMCA5 protein structure using experimental restraints obtained by XLMS. The experimental design for novel methods and the final protocol provided here can guide studies with other metacaspases. The production of TcMCA5 allows further investigations as protein crystallography, HTS drug discovery to create potential therapeutic in the treatment of Chagas' disease and in the way to clarify how the PCD works in the parasite., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Motivation: Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample., Results: We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate our software's usefulness by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL's clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software., Availabilityand Implementation: QUIN-XL and a user tutorial are freely available at http://patternlabforproteomics.org/quinxl for academic users., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

A peptide from the P0 acidic ribosomal protein (pP0) of ticks conjugated to keyhole limpet hemocyanin from Megathura crenulata has shown to be effective against different tick species when used in host vaccination. Turning this peptide into a commercial anti-tick vaccine will depend on finding the appropriate, technically and economically feasible way to present it to the host immune system. Two conjugates (p64K-Cys 1 pP0 and p64K-βAla 1 pP0) were synthesized using the p64K carrier protein from Neisseria meningitidis produced in Escherichia coli, the same cross-linking reagent, and two analogues of pP0. The SDS-PAGE analysis of p64K-Cys 1 pP0 showed a heterogeneous conjugate compared to p64K-βAla 1 pP0 that was detected as a protein band at 91kDa. The pP0/p64K ratio determined by MALDI-MS for p64K-Cys 1 pP0 ranged from 1 to 8, being 3-5 the predominant ratio, while in the case of p64K-βAla 1 pP0 this ratio was 5-7. Cys 1 pP0 was partially linked to 35 out of 39 Lys residues and the N-terminal end, while βAla 1 pP0 was mostly linked to the six free cysteine residues, to the N-terminal end, and, in a lesser extent, to Lys residues. The assignment of the conjugation sites and side reactions were based on the identification of type 2 peptides. Rabbit immunizations showed the best anti-pP0 titers and the highest efficacy against Rhipicephalus sanguineus ticks when the p64K-Cys 1 pP0 was used as vaccine antigen. The presence of high molecular mass aggregates observed in the SDS-PAGE analysis of p64K-Cys 1 pP0 could be responsible for a better immune response against pP0 and consequently for its better efficacy as an anti-tick vaccine. Graphical abstract., (© 2021. Springer-Verlag GmbH Germany, part of Springer Nature.)

In proteomics, the identification of peptides from mass spectral data can be mathematically described as the partitioning of mass spectra into clusters (i.e., groups of spectra derived from the same peptide). The way partitions are validated is just as important, having evolved side by side with the clustering algorithms themselves and given rise to many partition assessment measures. An assessment measure is said to have a selection bias if, and only if, the probability that a randomly chosen partition scoring a high value depends on the number of clusters in the partition. In the context of clustering mass spectra, this might mislead the validation process to favor clustering algorithms that generate too many (or few) spectral clusters, regardless of the underlying peptide sequence. A selection bias toward the number of peptides is desirable for proteomics as it estimates the number of peptides in a complex protein mixture. Here, we introduce an assessment measure that is purposely biased toward the number of peptide ion species. We also introduce a partition assessment framework for proteomics, called the Partition Assessment Tool, and demonstrate its importance by evaluating the performance of eight clustering algorithms on seven proteomics datasets while discussing the trade-offs involved. SIGNIFICANCE: Clustering algorithms are widely adopted in proteomics for undertaking several tasks such as speeding up search engines, generating consensus mass spectra, and to aid in the classification of proteomic profiles. Choosing which algorithm is most fit for the task at hand is not simple as each algorithm has advantages and disadvantages; furthermore, specifying clustering parameters is also a necessary and fundamental step. For example, deciding on whether to generate "pure clusters" or fewer clusters but accepting noise. With this as motivation, we verify the performance of several widely adopted algorithms on proteomic datasets and introduce a theoretical framework for drawing conclusions on which approach is suitable for the task at hand., (Copyright © 2021 Elsevier B.V. All rights reserved.)

We present RawVegetable, a software for mass spectrometry data assessment and quality control tailored toward shotgun proteomics and cross-linking experiments. RawVegetable provides four main modules with distinct features: (A) The charge state chromatogram that independently displays the ion current for each charge state; useful for optimizing the chromatography for highly charged ions and with lower XIC values such as those typically found in cross-linking experiments. (B) The XL-Artefact determination, which flags possible noncovalently associated peptides. (C) The TopN density estimation, for detecting retention time intervals of under or over-sampling, and (D) The chromatography reproducibility module, which provides pairwise comparisons between multiple experiments. RawVegetable, a tutorial, and the example data are freely available for academic use at: http://patternlabforproteomics.org/rawvegetable. SIGNIFICANCE: Chromatography optimization is a critical step for any shotgun proteomic or cross-linking mass spectrometry experiment. Here, we present a nifty solution with several key features, such as displaying individual charge state chromatograms, highlighting chromatographic regions of under- or over-sampling and checking for reproducibility., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020 Elsevier B.V. All rights reserved.)

We present the Mixed-Data Acquisition (MDA) strategy for mass spectrometry data acquisition. MDA combines Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) in the same run, thus doing away with the requirements for separate DDA spectral libraries. MDA is a natural result from advances in mass spectrometry, such as high scan rates and multiple analyzers, and is tailored toward exploiting these features. We demonstrate MDA's effectiveness on a yeast proteome analysis by overcoming a common bottleneck for XIC-based label-free quantitation; namely, the coelution of precursors when m/z values cannot be distinguished. We anticipate that MDA will become the next mainstream data generation approach for proteomics. MDA can also serve as an orthogonal validation approach for DDA experiments. Specialized software for MDA data analysis is made available on the project's website., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Motivation: We present the first tool for unbiased quality control of top-down proteomics datasets. Our tool can select high-quality top-down proteomics spectra, serve as a gateway for building top-down spectral libraries and, ultimately, improve identification rates., Results: We demonstrate that a twofold rate increase for two E. coli top-down proteomics datasets may be achievable., Availability and Implementation: http://patternlabforproteomics.org/tdgc, freely available for academic use., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use., (Copyright © 2019. Published by Elsevier B.V.)

Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus. To achieve this, we used isobaric labeling (iTRAQ) of peptides, a 10-step HILIC fractionation, and reversed-phase nano-chromatography coupled online with a Q-Exactive Plus mass spectrometer. We updated PatternLab to take advantage of the new Comet-PEFF search engine that enables identifying post-translational modifications and mutations included in neXtProt's PSI Extended FASTA Format (PEFF) metadata. Our pipeline then uses a text-mining tool that automatically extracts PubMed IDs from the proteomic result metadata and drills down keywords from manuscripts related with the biological processes at hand. Our results disclose important proteins such as apolipoprotein B-100, S100 and 14-3-3 proteins, among many others, highlighting the different pathways enriched by each cancer type., Significance: Gastric cancer is a heterogeneous and multifactorial disease responsible for a significant number of deaths every year. Despite the constant improvement of surgical techniques and multimodal treatments, survival rates are low, mostly due to limited diagnostic techniques and late symptoms. Intestinal and diffuse types of gastric cancer have distinct clinical and pathological characteristics; yet little is known about the molecular mechanisms regulating these two types of gastric tumors. Here we compared the proteomic profile of diffuse and intestinal types of gastric cancer from the same anatomical location, the corpus, from four male patients. This methodological design aimed to eliminate proteomic variations resulting from comparison of tumors from distinct anatomical regions. Our PEFF-tailored proteomic pipeline significantly increased the identifications as when compared to previous versions of PatternLab., (Copyright © 2017 Elsevier B.V. All rights reserved.)