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This study explores how the expression of feelings and the use of personal pronouns on Twitter are associated with user engagement. Unlike most previous studies which focused on the types of emotions that generate user engagement, it uses the volume-control model, which also considers the social dimension of power. Looking at the usage of pronouns, it examines the balance achieved between popular messages that target larger groups and personalized messages that target smaller groups and individuals. The findings show that there is a significant difference between the motivation to share (retweet) and to reply to a message. Users on Twitter tend to retweet messages with popular characteristics, addressing larger groups with positive feelings. On the other hand, replies were associated with more personalized messages and a greater use of negative feelings. Users with more followers and friends presented a balance between popularization and personalization techniques, as their tweets were associated with higher customization of the messages to specific groups yet avoided negative feelings.

In moth-pollinated petunias, production of floral volatiles initiates when the flower opens and occurs rhythmically during the day, for optimal flower–pollinator interaction. To characterize the developmental transcriptomic response to time of day, we generated RNA-Seq databases for corollas of floral buds and mature flowers in the morning and in the evening. Around 70% of transcripts accumulating in petals demonstrated significant changes in expression levels in response to the flowers’ transition from a 4.5-cm bud to a flower 1 day postanthesis (1DPA). Overall, 44% of the petal transcripts were differentially expressed in the morning vs. evening. Morning/evening changes were affected by flower developmental stage, with a 2.5-fold larger transcriptomic response to daytime in 1DPA flowers compared to buds. Analyzed genes known to encode enzymes in volatile organic compound biosynthesis were upregulated in 1DPA flowers vs. buds—in parallel with the activation of scent production. Based on analysis of global changes in the petal transcriptome, PhWD2 was identified as a putative scent-related factor. PhWD2 is a protein that is uniquely present in plants and has a three-domain structure: RING–kinase–WD40. Suppression of PhWD2 (termed UPPER - Unique Plant PhEnylpropanoid Regulator) resulted in a significant increase in the levels of volatiles emitted from and accumulated in internal pools, suggesting that it is a negative regulator of petunia floral scent production.

With multiple PD-(L)1 inhibitors approved across dozens of indications by the US Food and Drug Administration, the number of patients exposed to these agents in adjuvant, first-line metastatic, second-line metastatic, and refractory treatment settings is increasing rapidly. Although some patients will experience durable benefit, many have either no clinical response or see their disease progress following an initial response to therapy. There is a significant need to identify therapeutic approaches to overcome resistance and confer clinical benefits for these patients. PD-1 pathway blockade has the longest history of use in melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC). Therefore, these settings also have the most extensive clinical experience with resistance. In 2021, six non-profit organizations representing patients with these diseases undertook a year-long effort, culminating in a 2-day workshop (including academic, industry, and regulatory participants) to understand the challenges associated with developing effective therapies for patients previously exposed to anti-PD-(L)1 agents and outline recommendations for designing clinical trials in this setting. This manuscript presents key discussion themes and positions reached through this effort, with a specific focus on the topics of eligibility criteria, comparators, and endpoints, as well as tumor-specific trial design options for combination therapies designed to treat patients with melanoma, NSCLC, or RCC after prior PD-(L)1 pathway blockade.

Summary: Background: The optimal timing for SARS-CoV-2 vaccines within the first year after allogeneic hematopoietic cell transplant (HCT) is poorly understood. Methods: We conducted a prospective, multicentre, observational study of allogeneic HCT recipients who initiated SARS-CoV-2 vaccinations within 12 months of HCT. Participants were enrolled at 22 academic cancer centers across the United States. Participants of any age who were planning to receive a first post-HCT SARS-CoV-2 vaccine within 12 months of HCT were eligible. We obtained blood prior to and after each vaccine dose for up to four vaccine doses, with an end-of-study sample seven to nine months after enrollment. We tested for SARS-CoV-2 spike protein (anti-S) IgG; nucleocapsid protein (anti-N) IgG; neutralizing antibodies for Wuhan D614G, Delta B.1.617.2, and Omicron B.1.1.529 strains; and SARS-CoV-2-specific T-cell receptors (TCRs). The primary outcome was a comparison of anti-S IgG titers at the post-V2 time point in participants initiating vaccinations

Immune-related adverse events (irAEs) associated with immune checkpoint inhibitor (ICI) therapy may vary substantially in their clinical presentation, including natural history, outcomes to treatment, and patterns. The application of clinical guidelines for irAE management can be challenging for practitioners due to a lack of common or consistently applied terminology. Furthermore, given the growing body of clinical experience and published data on irAEs, there is a greater appreciation for the heterogeneous natural histories, responses to treatment, and patterns of these toxicities, which is not currently reflected in irAE guidelines. Furthermore, there are no prospective trial data to inform the management of the distinct presentations of irAEs. Recognizing a need for uniform terminology for the natural history, response to treatment, and patterns of irAEs, the Society for Immunotherapy of Cancer (SITC) convened a consensus panel composed of leading international experts from academic medicine, industry, and regulatory agencies. Using a modified Delphi consensus process, the expert panel developed clinical definitions for irAE terminology used in the literature, encompassing terms related to irAE natural history (ie, re-emergent, chronic active, chronic inactive, delayed/late onset), response to treatment (ie, steroid unresponsive, steroid dependent), and patterns (ie, multisystem irAEs). SITC developed these definitions to support the adoption of a standardized vocabulary for irAEs, which will have implications for the uniform application of irAE clinical practice guidelines and to enable future irAE clinical trials.

Immunotherapy is the standard of care for several cancers and the field continues to advance at a rapid pace, with novel combinations leading to indications in an increasing number of disease settings. Durable responses and long-term survival with immunotherapy have been demonstrated in some patients, though lack of initial benefit and recurrence after extended disease control remain major hurdles for the field. Many new combination regimens are in development for patients whose disease progressed on initial immunotherapy. To guide clinical trial design and support analyses of emerging molecular and cellular data surrounding mechanisms of resistance, the Society for Immunotherapy of Cancer (SITC) previously generated consensus clinical definitions for resistance to single-agent anti-PD-1 immune checkpoint inhibitors (ICIs) in three distinct scenarios: primary resistance, secondary resistance, and progression after treatment discontinuation. An unmet need still exists, however, for definitions of resistance to ICI-based combinations, which represent an expanding frontier in the immunotherapy treatment landscape. In 2021, SITC convened a workshop including stakeholders from academia, industry, and government to develop consensus definitions for resistance to ICI-based combination regimens for improved outcome assessment, trial design and drug development. This manuscript reports the minimum drug exposure requirements and time frame for progression that define resistance in both the metastatic setting and the perioperative setting, as well as key caveats and areas for future research with ICI/ICI combinations. Definitions for resistance to ICIs in combination with chemotherapy and targeted therapy will be published in companion volumes to this paper.

Mucositis research and treatment are a rapidly evolving field providing constant new avenues of research and potential therapies. The MASCC/ISOO Mucositis Study Group regularly assesses available literature relating to pathogenesis, mechanisms, and novel therapeutic approaches and distils this to summary perspectives and recommendations. Reviewers assessed 164 articles published between January 2011 and June 2016 to identify progress made since the last review and highlight new targets for further investigation. Findings were organized into sections including established and emerging mediators of toxicity, potential insights from technological advances in mucositis research, and perspective. Research momentum is accelerating for mucositis pathogenesis, and with this has come utilization of new models and interventions that target specific mechanisms of injury. Technological advances have the potential to revolutionize the field of mucositis research, although focused effort is needed to move rationally targeted interventions to the clinical setting. [ABSTRACT FROM AUTHOR]

Abstract Background The epigenetic age can now be extrapolated from one of several epigenetic clocks, which are based on age-related changes in DNA methylation levels at specific multiple CpG sites. Accelerated aging, calculated from the discrepancy between the chronological age and the epigenetic age, has shown to predict morbidity and mortality rate. We assumed that deconvolution of epigenetic age to its components could shed light on the diversity of epigenetic, and by inference, on inter-individual variability in the causes of biological aging. Results Using the Horvath original epigenetic clock, we identified several CpG sites linked to distinct genes that quantitatively explain much of the inter-personal variability in epigenetic aging, with CpG sites related to secretagogin and malin being the most variable. We show that equal epigenetic age in different subjects can result from variable contribution size of the same CpG sites to the total epigenetic age. In a healthy cohort, the most variable CpG sites are responsible for accelerated and decelerated epigenetic aging, relative to chronological age. Conclusions Of the 353 CpG sites that form the basis for the Horvath epigenetic age, we have found the CpG sites that are responsible for accelerated and decelerated epigenetic aging in healthy subjects. However, the relative contribution of each site to aging varies between individuals, leading to variable personal aging patterns. Our findings pave the way to form personalized aging cards allowing the identification of specific genes related to CpG sites, as aging markers, and perhaps treatment of these targets in order to hinder undesirable age drifting.

Abstract Background The increased risk for cardiovascular events in diabetics is heterogeneous and contemporary clinical risk score calculators have limited predictive value. We therefore examined the additional value of coronary artery calcium score (CACS) in outcome prediction in type 2 diabetics without clinical coronary artery disease (CAD). Methods The study examined a population-based cohort of type 2 diabetics (n = 735) aged 55–74 years, recruited between 2006 and 2008. Patients had at least one additional risk factor and no history or symptoms of CAD. Risk assessment tools included Pooled Cohort Equations (PCE) and Multi-Ethnic Study of Atherosclerosis (MESA) 10-year risk score calculators and CACS. The occurrence of myocardial infarction (MI), stroke or cardiovascular death (MACE) was assessed over 10-years. Results Risk score calculators predicted MACE and MI and cardiovascular death individually but not stroke. Increasing levels of CACS predicted MACE and its components independently of clinical risk scores, glycated hemoglobin and other baseline variables: hazard ratio (95% confidence interval) 2.92 (1.06–7.86), 6.53 (2.47–17.29) and 8.3 (3.28–21) for CACS of 1–100, 101–300 and > 300 Agatston units respectively, compared to CACS = 0. Addition of CACS to PCE improved discrimination of MACE [AUC of PCE 0.615 (0.555–0.676) versus PCE + CACS 0.696 (0.642–0.749); p = 0.0024]. Coronary artery calcium was absent in 24% of the study population and was associated with very low event rates even in those with high estimated risk scores. Conclusions CACS in asymptomatic type 2 diabetics provides additional prognostic information beyond that obtained from clinical risk scores alone leading to better discrimination between risk categories.

With the rise in number of eukaryotic species being fully sequenced, large scale phylogenetic profiling can give insights on gene function, Here, the authors describe a machine-learning approach that integrates co-evolution across eukaryotic clades to predict gene function and functional interactions among human genes.

Background and Rationale: Immune checkpoint inhibitor (ICI) therapy is an expanding therapeutic option for hepatocellular carcinoma (HCC). Antibiotics (ATB) taken prior to or early during ICI therapy can impact immunotherapy efficacy across indications; however, the effect of ATB is undefined in HCC. Methods: In a large international cohort of 450 ICI recipients from Europe, North America, and Asia, we categorized patients according to timing of ATB focusing on exposure within −30 to +30 days from ICI (early immunotherapy period [EIOP]). EIOP was evaluated in association with overall survival (OS), progression-free survival (PFS), and best radiologic response using RECIST 1.1 criteria. Results: Our study comprised mostly cirrhotic (329, 73.3%) males (355, 79.1%) with a Child-Turcotte Pugh class of A (332, 73.9%), receiving ICI after 1 therapy line (251, 55.9%) for HCC of Barcelona clinic liver cancer stage C (325, 72.4%). EIOP (n = 170, 37.9%) was independent of baseline clinicopathologic features of HCC and correlated with longer PFS (6.1 vs. 3.7 months, log-rank p = 0.0135). EIOP+ patients had similar OS, overall response, and disease control rates (DCRs) compared to EIOP. The effect of EIOP persisted in landmark time analyses and in multivariable models, confirming the independent predictive role of EIOP in influencing PFS following adjustment for covariates reflective of tumor burden, liver function, and ICI regimen administered. In patients receiving programmed cell death-1 receptor/ligand inhibitors monotherapy, EIOP was also associated with higher DCRs (61.4% vs. 50.9%, p = 0.0494). Conclusions: Unlike other oncological indications, ATB in the 30 days before or after ICI initiation is associated with improved benefit from immunotherapy, independent of disease and treatment-related features. Evaluation of the immune microbiologic determinants of response to ICI in HCC warrants further investigation.

Background The Food and Drug Administration recommends that people living with HIV (PWH) with a CD4+ T cell count (CD4) ≥350 cells/µL may be eligible for any cancer clinical trial, but there is reluctance to enter patients with lower CD4 counts into cancer studies, including immune checkpoint inhibitor (ICI) studies. Patients with relapsed or refractory cancers may have low CD4 due to prior cancer therapies, irrespective of HIV status. It is unclear how baseline CD4 prior to ICI impacts the proportion of treatment-emergent adverse events (TEAE) and whether it differs by HIV status in ICI treated patients.Methods We conducted a pilot retrospective cohort study of participants eligible for ICI for advanced cancers from three phase 1/2 trials in the USA and Spain. We determined whether baseline CD4 counts differed by HIV status and whether the effect of CD4 counts on incidence of TEAE was modified by HIV status using a multivariable logistic regression model.Results Of 122 participants, 66 (54%) were PWH who received either pembrolizumab or durvalumab and 56 (46%) were HIV-negative who received bintrafusp alfa. Median CD4 at baseline was 320 cells/µL (IQR 210–495) among PWH and 356 cells/µL (IQR 260–470) among HIV-negative participants (p=0.5). Grade 3 or worse TEAE were recorded among 7/66 (11%) PWH compared with 7/56 (13%) among HIV-negative participants. When adjusted for prior therapies, age, sex, and race, the effect of baseline CD4 on incidence of TEAE was not modified by HIV status for any TEAE (interaction term p=0.7), or any grade ≥3 TEAE (interaction term p=0.1).Conclusions There was no significant difference in baseline CD4 or the proportions of any TEAE and grade ≥3 TEAE by HIV status. CD4 count thresholds for cancer clinical trials should be carefully reviewed to avoid unnecessarily excluding patients with HIV and cancer.

Water distribution network design is a complex multi-objective optimization problem and multi-objective evolutionary algorithms (MOEAs) such as NSGA II have been widely used to solve this optimization problem. However, as networks get larger, NSGA II struggles to find the diverse and uniform solutions that are critical in multi-objective optimization. This research proposes an improved version of NSGA II that uses three new-generation methods to target different regions of the Pareto front and thus increase the number of solutions in critical regions. These methods include saving an archive, local search around extreme and uncrowded Pareto front, and local search around the knee area of the Pareto front. The improved NSGA II is tested on benchmark networks of different sizes and compared to the best-known Pareto front of the networks determined by MOEAs. The results show that the proposed algorithm outperforms the original NSGA II in terms of broadening the Pareto front solution range, increasing solution density, and discovering more non-dominated solutions. The improved NSGA II can find solutions that cover all parts of the Pareto front using a single algorithm without increasing computational effort.

Introduction: Older patients who arrive to the emergency room with delirium have a worse prognosis than others. Early detection and treatment of this problem has been shown to improve outcome. We have launched a project at our hospital to improve the care of patients who arrive delirious to the medical emergency room. The present article describes lessons that can be learned from this pilot initiative. Methods: All patients older than 70 years admitted to the department of internal medicine were screened for delirium in the emergency room using the 4AT screening tool. Data of patients with a 4AT score ≥5 (or with incomplete score) were transferred to the geriatric unit of the hospital. On the ward, the presence of delirium was confirmed by a geriatric nurse that validated that the patient could walk with support and ordered mobilization and physiotherapy (M&P). Results: Over the 2 and a half years (10 quarters) allocated for the pilot project, 1,078 medical patients with delirium were included in this survey. In 59.3%, the diagnosis of delirium could be confirmed only after admission. Due to budgetary constraints, only 54.7% received the allocated specific intervention – early M&P. Since it was decided that randomization was not appropriate for our initiative, we found that patients who received M&P had lower (better) 4AT scores on admission, and lower mortality. No significant difference was found between the patients who received M&P and the others in length of hospitalization and discharge to nursing homes. Retrospective comparison of the two groups did not enable to determine whether M&P was given to the patients for whom it was most effective. Conclusions: It is often not possible to verify in the emergency room that the cognitive decline is indeed new, that is, is due to delirium, and measures must be taken to verify this point as soon as possible after admission. Due to numerous constraints, the availability of early M&P is often insufficient. Whenever resources are scarce and randomization is avoided, adequate criteria should be found for allocating existing dedicated staff to patients for whom early mobilization is likely to be most beneficial.

Summary: Animals traveling on a horizontal surface stabilize their head in relation to the substrate in order to gather spatial information and orient. What, however, do they do when traveling on an incline? We examined how three rodent species differing in motor abilities and habitats explore a platform tilted at 0–90°, hypothesizing that they would attempt to maintain bilateral vestibular cues. We found that traveling up or down was mainly straight vertically rather than diagonally, which results in identical bilateral vestibular cues. This was also achieved when traveling horizontally through rotating the head to parallel the horizontal plane. Traveling diagonally up or down was avoided, perhaps due to different bilateral vestibular cues that could hinder orientation. Accordingly, we suggest that maintaining identical bilateral cues is an orientational necessity that overrides differences in motor abilities and habitats, and that this necessity is a general characteristic of animals in motion.

Abstract Background Coronavirus disease 2019 (COVID-19) has no confirmed specific treatments. However, there might be in vitro and early clinical data as well as evidence from severe acute respiratory syndrome and Middle Eastern respiratory syndrome that could inform clinicians and researchers. This systematic review aims to create priorities for future research of drugs repurposed for COVID-19. Methods This systematic review will include in vitro, animal, and clinical studies evaluating the efficacy of a list of 34 specific compounds and 4 groups of drugs identified in a previous scoping review. Studies will be identified both from traditional literature databases and pre-print servers. Outcomes assessed will include time to clinical improvement, time to viral clearance, mortality, length of hospital stay, and proportions transferred to the intensive care unit and intubated, respectively. We will use the GRADE methodology to assess the quality of the evidence. Discussion The challenge posed by COVID-19 requires not just a rapid review of drugs that can be repurposed but also a sustained effort to integrate new evidence into a living systematic review. Trial registration PROSPERO 2020 CRD42020175648

Objectives: We aimed to examine the relationships between body mass index (BMI) and metabolic syndrome (MS) components as a function of age and gender across weight categories. Methods: This cross-sectional study included 19,328 subjects who participated in a health-screening program. We analyzed 14,093 apparently healthy subjects with a BMI ≥ 18.5 kg/m2 (ranging from 18.5 to 46 kg/m2). Results: At a BMI of 18.5 kg/m2, 16% of subjects had one or more MS components (MS ≥ 1). The number of MS components increased linearly with BMI. The most prevalent components for MS1-4 were hypertension (in men) and increased waist circumference (in women). Among 6391 non-obese subjects with MS = 0, there was a linear increase in blood pressure, glucose, and triglycerides, as well as a decline in high-density lipoprotein cholesterol, as BMI increased. In 2087 subjects with a BMI ≥ 30 kg/m2, a true normometabolic state (MS = 0) was observed in only 7.5%, declining to less than 1% at a BMI ≥ 36 kg/m2 (ATP criteria). Women were metabolically protected relative to men between the ages of 30 and 50 years. Conclusions: (A) MS components increase linearly with BMI from the lowest normal BMI and continue to increase with age and BMI; (B) metabolically healthy obesity is rare in subjects with a high BMI and declines with age; (C) hypertension is the most common component in men; and (D) in women, MS components are seen at older ages than in men for the same BMI. Metabolic health declines with age and BMI in nearly all subjects with obesity.

AbstractA key limitation in current datasets for multi-hop reasoning is that the required steps for answering the question are mentioned in it explicitly. In this work, we introduce StrategyQA, a question answering (QA) benchmark where the required reasoning steps are implicit in the question, and should be inferred using a strategy. A fundamental challenge in this setup is how to elicit such creative questions from crowdsourcing workers, while covering a broad range of potential strategies. We propose a data collection procedure that combines term-based priming to inspire annotators, careful control over the annotator population, and adversarial filtering for eliminating reasoning shortcuts. Moreover, we annotate each question with (1) a decomposition into reasoning steps for answering it, and (2) Wikipedia paragraphs that contain the answers to each step. Overall, StrategyQA includes 2,780 examples, each consisting of a strategy question, its decomposition, and evidence paragraphs. Analysis shows that questions in StrategyQA are short, topic-diverse, and cover a wide range of strategies. Empirically, we show that humans perform well (87%) on this task, while our best baseline reaches an accuracy of ∼ 66%.

Background The combination of antiangiogenic agents with immune checkpoint inhibitors could potentially overcome immune suppression driven by tumor angiogenesis. We report results from a phase IB study of ziv-aflibercept plus pembrolizumab in patients with advanced solid tumors.Methods This is a multicenter phase IB dose-escalation study of the combination of ziv-aflibercept (at 2–4 mg/kg) plus pembrolizumab (at 2 mg/kg) administered intravenously every 2 weeks with expansion cohorts in programmed cell death protein 1 (PD-1)/programmed death-ligand 1(PD-L1)-naïve melanoma, renal cell carcinoma (RCC), microsatellite stable colorectal cancer (CRC), and ovarian cancer. The primary objective was to determine maximum tolerated dose (MTD) and recommended dose of the combination. Secondary endpoints included overall response rate (ORR) and overall survival (OS). Exploratory objectives included correlation of clinical efficacy with tumor and peripheral immune population densities.Results Overall, 33 patients were enrolled during dose escalation (n=3) and dose expansion (n=30). No dose-limiting toxicities were reported in the initial dose level. Ziv-aflibercept 4 mg/kg plus pembrolizumab 2 mg/kg every 2 weeks was established as the MTD. Grade ≥3 adverse events occurred in 19/33 patients (58%), the most common being hypertension (36%) and proteinuria (18%). ORR in the dose-expansion cohort was 16.7% (5/30, 90% CI 7% to 32%). Complete responses occurred in melanoma (n=2); partial responses occurred in RCC (n=1), mesothelioma (n=1), and melanoma (n=1). Median OS was as follows: melanoma, not reached (NR); RCC, 15.7 months (90% CI 2.5 to 15.7); CRC, 3.3 months (90% CI 0.6 to 3.4); ovarian, 12.5 months (90% CI 3.8 to 13.6); other solid tumors, NR. Activated tumor-infiltrating CD8 T cells at baseline (CD8+PD1+), high CD40L expression, and increased peripheral memory CD8 T cells correlated with clinical response.Conclusion The combination of ziv-aflibercept and pembrolizumab demonstrated an acceptable safety profile with antitumor activity in solid tumors. The combination is currently being studied in sarcoma and anti-PD-1-resistant melanoma.Trial registration number NCT02298959.

Understanding the synchronization of human networks is important in many aspects, but current research is suffering from limited control and noisy environments. Shahal et al. show a quantitative study with full control over the network connectivity, coupling strength and delay among interacting violin players.

Abstract Geographical variability of cancer burden was almost exclusively estimated for common cancers. Since rare cancers (RC) have become an area of priority for basic and clinical research and public health organizations, this paper provides, using a common methodology, a detailed comparison of incidence and survival for RC in the US and Europe. We estimated incidence and net survival of 199 malignant RC from data of 2 580 000 patients collected by 18 US‐SEER and 94 European registries, diagnosed within the most recent common period 2000‐2007. RC were defined according to the criterion of crude annual incidence rates 65+ years of age. Use of standardized methods evidenced that incidence and survival rate of majority of RC were higher in the United States compared to Europe. Possible reasons for such differences, requiring further studies, include distribution of risk factors, ability to diagnose RC, different registration practices, and use of updated International Classification of Diseases for Oncology.

Objective: Speech tests assess the ability of people with hearing loss to comprehend speech with a hearing aid or cochlear implant. The tests are usually at the word or sentence level. However, few tests analyze errors at the phoneme level. So, there is a need for an automated program to visualize in real time the accuracy of phonemes in these tests.Method: The program reads in stimulus-response pairs and obtains their phonemic representations from an open-source digital pronouncing dictionary. The stimulus phonemes are aligned with the response phonemes via a modification of the Levenshtein Minimum Edit Distance algorithm. Alignment is achieved via dynamic programming with modified costs based on phonological features for insertion, deletions and substitutions. The accuracy for each phoneme is based on the F1-score. Accuracy is visualized with respect to place and manner (consonants) or height (vowels). Confusion matrices for the phonemes are used in an information transfer analysis of ten phonological features. A histogram of the information transfer for the features over a frequency-like range is presented as a phonemegram.Results: The program was applied to two datasets. One consisted of test data at the sentence and word levels. Stimulus-response sentence pairs from six volunteers with different degrees of hearing loss and modes of amplification were analyzed. Four volunteers listened to sentences from a mobile auditory training app while two listened to sentences from a clinical speech test. Stimulus-response word pairs from three lists were also analyzed. The other dataset consisted of published stimulus-response pairs from experiments of 31 participants with cochlear implants listening to 400 Basic English Lexicon sentences via different talkers at four different SNR levels. In all cases, visualization was obtained in real time. Analysis of 12,400 actual and random pairs showed that the program was robust to the nature of the pairs.Conclusion: It is possible to automate the alignment of phonemes extracted from stimulus-response pairs from speech tests in real time. The alignment then makes it possible to visualize the accuracy of responses via phonological features in two ways. Such visualization of phoneme alignment and accuracy could aid clinicians and scientists.

Objective The vast majority of known proteins have not been experimentally tested even at the level of measuring their expression, and the function of many proteins remains unknown. In order to decipher protein function and examine functional associations, we developed "Cliquely", a software tool based on the exploration of co-occurrence patterns. Computational model Using a set of more than 23 million proteins divided into 404,947 orthologous clusters, we explored the co-occurrence graph of 4,742 fully sequenced genomes from the three domains of life. Edge weights in this graph represent co-occurrence probabilities. We use the Bron–Kerbosch algorithm to detect maximal cliques in this graph, fully-connected subgraphs that represent meaningful biological networks from different functional categories. Main results We demonstrate that Cliquely can successfully identify known networks from various pathways, including nitrogen fixation, glycolysis, methanogenesis, mevalonate and ribosome proteins. Identifying the virulence-associated type III secretion system (T3SS) network, Cliquely also added 13 previously uncharacterized novel proteins to the T3SS network, demonstrating the strength of this approach. Cliquely is freely available and open source. Users can employ the tool to explore co-occurrence networks using a protein of interest and a customizable level of stringency, either for the entire dataset or for a one of the three domains—Archaea, Bacteria, or Eukarya.

Human pluripotent stem cells (hPSC) can be directed to differentiate in vitro into insulin-prorducing beta cells (SC-β). Although these cells accurately respond to glucose and can reverse diabetes in preclinical models improvments in the final cell products are desirable. For example, safety, controlling the cellular compositions and protection against immune rejection may be addressed by genetic modifications of SC-β pre-transplantation. To screen for gene targets, we have generated a human embryonic stem cell line (hESC) that constitutively express the enhanced specificity Streptococcus pyogenes Cas9 (eSpCas9) gene, knocked-in into the GAPDH locus.

The vastness of water distribution systems (WDS) makes them vulnerable to exposure to different types of accidental/intentional contamination. Although most such contamination events that occurred in the recent past were accidental, criminal intent was involved in a few. Considering the accessibility of WDS and the potentially harmful outcomes of drinking-water contamination, online water-quality monitoring sensors are typically positioned in selected locations throughout WDS as a preventive strategy. These sensors, once positioned, communicate over a cyber-infrastructure layer and are liable to cyber-physical attacks—the sensor and/or its communication system becoming compromised or the sensor network becoming malfunctioned such that part of its components is deactivated. However, the sensor network placement state-of-the-art has thus far overlooked these cyber-physical attack scenarios. The current study attempts to overcome this limitation in the state-of-the-art by developing and demonstrating a methodology for evaluating the impact of a cyber-physical attack on a sensor network, compromising its functionality partially. Our proof-of-concept, using a simple network and a straightforward cyber-physical attack scenario, has revealed the vast potential of examining the performance of sensor networks under accidental/intentional malfunctioning and providing valuable information for decision makers in water utilities and regulators.