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Saccharomyces pastorianus is an industrial natural yeast evolved from different hybridisation events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus. This complex aneuploid hybrid carries multiple copies of the parental alleles alongside specific hybrid genes and encodes for multiple protein isoforms which impart novel phenotypes, such as the strong ability to ferment at low temperature. These characteristics lead to agonistic or antagonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism. Here, we investigated the transcriptional signature of the different orthologous alleles in S. pastorianus during temperature shifts. We identified temperature-dependent media-independent genes and showed that 35% have their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. The analysis of the expression of ortholog parental alleles unveiled that the majority of the genes express preferentially one parental allele over the other, and that S. eubayanus-like alleles are significantly over-represented among the genes involved in cold acclimatisation. The presence of functionally redundant parental alleles may impact on the nature of protein complexes established in the hybrid, where both parental alleles are competing. Our expression data indicate that the majority of the protein complexes in the hybrid are likely to be either exclusively chimeric or uni-specific, and that the redundancy is discouraged, a scenario which fits well with the stoichiometric balance-hypothesis. This study offers the first overview of the transcriptional pattern of S. pastorianus and provide a rationalisation for its unique industrial traits at expression level. more...

Research Objectives Examine onabotulinumtoxinA utilization in patients with upper limb (UL) and lower limb (LL) spasticity from the Adult Spasticity International Registry (ASPIRE) study to gain real-world insights into the treatment of spastic hemiparesis. Design Prospective, observational registry (NCT01930786). Setting International clinical sites. Participants Adults with spasticity across multiple etiologies. Interventions OnabotulinumtoxinA at the clinician's discretion. Main Outcome Measures OnabotulinumtoxinA utilization and safety data were collected at each treatment session. Patients with spastic hemiparesis were defined as receiving ≥ 1 UL treatment and ≥ 1 LL treatment during the study. Results ASPIRE patients (N=730) were on average 53.6 years old, 52%; female, 77% Caucasian, 37% naive to botulinum toxin(s) for spasticity, and 56% post-stroke. Of N=730, n=284 patients were defined as hemiparetic. In hemiparetic patients treated for UL and LL at the same session (n=275), the mean total dose of onabotulinumtoxinA was 477 U for UL+LL, 257 U for UL, and 220 U for LL. Of n=275 hemiparetic patients, 56%; had a treatment interval of 10-15 weeks, 62% had 5-15 injections/session, and 82% had >5 muscles injected/session. Clenched fist was the most common UL presentation (n=219 patients), with 55% of sessions to the left side only. Equinovarus foot was the most common LL presentation (n=238 patients), with 52% of sessions to the left side only. Of the hemiparetic population (n=284), 115 patients (41%) reported 375 adverse events; 42 patients (15%) reported 80 serious adverse events. No new safety signals were identified. Conclusions This preliminary analysis from ASPIRE provides valuable, real-world evidence on the use of onabotulinumtoxinA to treat patients with combined upper limb and lower limb spasticity. OnabotulinumtoxinA was most frequently utilized to treat clenched fist (UL) and equinovarus foot (LL) in patients with spastic hemiparesis. Author(s) Disclosures Bavikatte: Consultant for Allergan(AbbVie); Francisco: Consulted/research grants from Allergan(AbbVie), Merz, and Ipsen; Esquenazi: Consulted for Allergan(AbbVie), Ipsen, and Merz. Received research grants from Allergan(AbbVie) and Ipsen; Dimyan: None reported; Ngo: None reported; Schwartz: Statistical consultant for Allergan(AbbVie); Zuzek: AbbVie employee; Jost: Speaker/consultant for Allergan(AbbVie), Ipsen, and Merz. more...

Osteocytes are mechanosensitive cells that control bone remodeling in response to mechanical loading. To date, specific signaling pathways modulated by mechanical loading in osteocytes are not well understood. Yes associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), the main effectors of the Hippo pathway, are reported to play a role in mechanotransduction and during osteoblastogenesis. Here, we hypothesized that YAP/TAZ signaling mediates osteocyte mechanosensing to target genes of the bone remodeling process. We aimed to investigate the contribution of YAP/TAZ in modulating the gene expression in an osteocyte-like cell line MLO-Y4. We developed a 3D osteocyte compression culture model from an MLO-Y4 osteocyte cell line embedded in concentrated collagen hydrogel. 3D-mechanical loading led to the increased expression of mechanosensitive genes and a subset of chemokines, including M-csf, Cxcl1, Cxcl2, Cxcl3, Cxcl9, and Cxcl10. The transcription regulators YAP and TAZ translocated to the nucleus and upregulated their target genes and proteins. RNAseq analysis revealed that YAP/TAZ knockdown mediated the regulation of several genes including osteocyte dendrite formation. Use of YAP/TAZ knockdown partially blunted the increase in M-csf and Cxcl3 levels in response to MLO-Y4 compression. These findings demonstrate that YAP/TAZ signaling is required for osteocyte-like cell mechano-transduction, regulates the gene expression profiles and controls chemokine expression. more...

PURPOSE: To evaluate timing and outcomes of BRCA testing and definitive surgical treatment among patients with newly diagnosed breast cancer. METHODS: Patient-reported (n = 1,381) and deidentified health-plan (n = 2,369) data were analyzed from a consecutive national series of 3,750 women whose healthcare providers ordered BRCA testing between March 2014 and June 2015, within 1 year following breast cancer diagnosis. RESULTS: Among 1,209 respondents, 54.4% received the genetic test results presurgery, 23.2% tested presurgery but received the results postsurgery, and 22.3% tested postsurgery. Patients aware of mutation-positive results presurgery were more likely to choose bilateral mastectomy (BLM) (n = 32/37) compared with patients who learned of positive results postsurgery (n = 14/32), (odds ratio [OR] = 8.23, 95% CI = 2.55 to 26.59, P < .001). When compared with women tested postsurgery, only women unaware of negative results presurgery had higher BLM rates (adjusted OR = 1.70, 95% CI = 1.07 to 2.69, P = .02). Among women > 50 tested presurgery, those unaware of negative results presurgery were more likely to choose BLM (n = 28/81) compared with those aware of negative results (n = 32/168) (OR = 2.25, 95% CI = 1.23 to 4.08, negative results awareness × age interaction, and P = .007). CONCLUSION: Nearly half of participants did not receive BRCA results presurgery, which limited their ability to make fully informed surgical treatment decisions. This may represent suboptimal care for unaware mutation-positive patients compared with those who were aware presurgery. Women > 50 who test negative are significantly less likely to choose BLM, a costly surgery that does not confer survival advantage, if they are aware of negative results presurgery. These results have important implications for quality of care and costs in the US health system. more...

Health and safety concerns during the COVID-19 pandemic required many face-to-face United States schools to suddenly shut their doors, moving classes to virtual learning environments. Amidst concerns of technology overuse, adolescents across the country saw dramatic increases in both personal screen time use and social isolation as they learned to navigate online schooling. Understanding the impact of the pandemic-related shutdowns upon adolescent well-being, learning, and social life is critical for designing effective online learning experiences, but research provides few insights from the adolescent perspective. This mixed methods study works to fill this gap by investigating adolescent needs and perceptions during the pandemic. The main questions asked are:To what extent does adolescent well-being during the pandemic differ from pre-pandemic well-being?What factors do adolescents view as influences upon their learning during the imposed shift to online schooling?What social changes and concerns do adolescents report during the pandemic? Twenty-one adolescents completed Likert scale surveys and participated in semi-structured one-to-one interviews. Results showed a significant decrease in positive affect and a significant increase in negative affect during the pandemic, suggesting a decline in well-being. The majority of participants reported high distractibility and noted the lure of entertaining technology, but also described their smartphones as "connecting" and "necessary". Social interactions were a priority for all participants, but participants agreed that opportunities for social connectedness in online education were limited. The challenges of online learning, the importance of identifying and responding to student needs, and suggested strategies for online education are discussed. more...

When Saccharomyces cerevisiae undergoes heat stress it stimulates several changes that are necessary for its survival, notably in carbon metabolism. Notable changes include increase in trehalose production and glycolytic flux. The increase in glycolytic flux has been postulated to be due to the regulatory effects in upper glycolysis, but this has not been confirmed. Additionally, trehalose is a useful industrial compound for its protective properties. A model of trehalose metabolism in S. cerevisiae was constructed using Convenient Modeller, a software that uses a combination of convenience kinetics and a genetic algorithm. The model was parameterized with quantitative omics under standard conditions and validated using data collected under heat stress conditions. The completed model was used to show that feedforward activation of pyruvate kinase by fructose 1,6-bisphosphate during heat stress contributes to the increase in metabolic flux. We were also able to demonstrate in silico that overexpression of enzymes involved in production and degradation of trehalose can lead to higher trehalose yield in the cell. By integrating quantitative proteomics with metabolic modelling, we were able to confirm that the flux increase in trehalose metabolic pathways during heat stress is due to regulatory effects and not purely changes in enzyme expression. The overexpression of enzymes involved in trehalose metabolism is a potential approach to be exploited for trehalose production without need for increasing temperature. more...

Genome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavor profiles are now a major ambition and challenge in craft brewing and distilling industries. Moreover, no genome annotation for most of these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. Our benchmark studies showed that HybridMine produced biologically accurate results for hybrid genomes compared to other well-established software. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl, and Bash programming languages and is available in GitHub. more...

Photosynthesis is especially sensitive to environmental conditions, and the composition of the photosynthetic apparatus can be modulated in response to environmental change, a process termed photosynthetic acclimation. Previously, we identified a role for a cytosolic fumarase, FUM2 in acclimation to low temperature in Arabidopsis thaliana. Mutant lines lacking FUM2 were unable to acclimate their photosynthetic apparatus to cold. Here, using gas exchange measurements and metabolite assays of acclimating and non-acclimating plants, we show that acclimation to low temperature results in a change in the distribution of photosynthetically fixed carbon to different storage pools during the day. Proteomic analysis of wild-type Col-0 Arabidopsis and of a fum2 mutant, which was unable to acclimate to cold, indicates that extensive changes occurring in response to cold are affected in the mutant. Metabolic and proteomic data were used to parameterize metabolic models. Using an approach called flux sampling, we show how the relative export of triose phosphate and 3-phosphoglycerate provides a signal of the chloroplast redox state that could underlie photosynthetic acclimation to cold. more...

Network analysis was used as a method to investigate the relationship between benthic macroinvertebrates in an urban river watershed and physicochemical variables. The measured physicochemical variables were the dissolved oxygen, temperature, nutrients, conductivity, pH, total organic matter, biochemical oxygen demand and river discharge. The metrics applied in the study were the degree of connections between nodes, the number of edges identified for each study location and the functional feeding groups. The river sampling took place over 14 months and sampling took place at five sites, two of which were upstream of a major wastewater treatment works and three sites were downstream of the works. A biological and environmental (BIOENV) analysis was included as part of the overall analysis to compare the variables that influenced the river ecosystem. This study shows that the relationships between benthic macroinvertebrates were stronger at the upstream locations of the watershed, while the downstream locations were controlled by the physicochemical relationships. From this analysis, the river quality and biodiversity were mainly controlled by the discharge, conductivity and availability of relevant organic matter suitable for organisms. Through the network, the degree of connections between the variables revealed the status of the urban river and provided insight into the possible management of vegetation cover across the urban watershed. more...

SummaryPlants acclimate their photosynthetic capacity in response to changing environmental conditions. In Arabidopsis thaliana, photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolic fumarase FUM2, however the role of this is currently unclear.In this study, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. Using physiological and biochemical analyses, we demonstrate that FUM2 is necessary for high as well as low temperature acclimation.To understand the role of FUM2 activity, we have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite. Its precursor, malate, is shown to be high-risk and liable to cause system instability. We conclude that the role of cytosolic fumarase, FUM2, is to provide a fail-safe, maintaining system stability under changing environmental conditions.We argue that FMEA is a technique which is not only useful in understanding plant metabolism, it can also be used to study reliability in other systems and aid the design of synthetic pathways. more...

The global spread of coronavirus disease 2019 (COVID-19) is overwhelming many health-care systems. As a result, epidemiological models are being used to inform policy on how to effectively deal with this pandemic. The majority of existing models assume random diffusion but do not take into account differences in the amount of interactions between individuals, i.e. the underlying human interaction network, whose structure is known to be scale-free. Here, we demonstrate how this network of interactions can be used to predict the spread of the virus and to inform policy on the most successful mitigation and suppression strategies. Using stochastic simulations in a scale-free network, we show that the epidemic can propagate for a long time at a low level before the number of infected individuals suddenly increases markedly, and that this increase occurs shortly after the first hub is infected. We further demonstrate that mitigation strategies that target hubs are far more effective than strategies that randomly decrease the number of connections between individuals. Although applicable to infectious disease modelling in general, our results emphasize how network science can improve the predictive power of current COVID-19 epidemiological models. more...

Background Inflammatory bowel disease (IBD) is associated with alterations of the innate and adaptive immune systems. Monocytes respond to inflammation and infection, yet the relationship between monocytosis and IBD severity is not fully understood. We aimed to characterize the prevalence of monocytosis in IBD and the association between monocytosis and disease severity and IBD-related health care utilization. Methods We used a multiyear, prospectively collected natural history registry to compare patients with IBD with monocytosis to those without monocytosis, among all patients and by disease type. Results A total of 1290 patients with IBD (64.1% with Crohn disease; 35.9% with ulcerative colitis) were included (mean age 46.4 years; 52.6% female). Monocytosis was found in 399 (30.9%) of patients with IBD (29.3% with Crohn disease; 33.9% with ulcerative colitis). Monocytosis was significantly associated with abnormal C-reactive protein level and erythrocyte sedimentation rate, anemia, worse quality of life, active disease, and increased exposure to biologics (all P < 0.001). Compared with patients without monocytosis, patients with monocytosis had a 3-fold increase in annual financial health care charges (median: $127,013 vs. $32,925, P < 0.001) and an increased likelihood of hospitalization (adjusted odds ratio [AOR], 4.5; P < 0.001), IBD-related surgery (AOR, 1.9; P = 0.002), and emergency department (ED) use (AOR, 2.8; P < 0.001). Patients with monocytosis had a shorter time to surgery, hospitalization, and ED visit after stratifying by disease activity (all P < 0.05). Conclusions Patients with IBD with monocytosis, regardless of disease type, are at increased risk for worse clinical outcomes, hospitalization, surgery, and ED use. Peripheral monocytosis may represent a routinely available biomarker of a distinct subgroup with severe disease. more...

Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavour profiles are now a major ambition and challenge in craft brewing and distilling industries. Genome-scale computational approaches are opening opportunities to model and predict favourable combination of traits for strain development. However, mining the genome of these complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. Moreover, no genome annotation for these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl and Bash programming languages and is available at https://github.com/Sookie-S/HybridMine. more...

BACKGROUND AND OBJECTIVES Many newly diagnosed breast cancer patients do not receive genetic counseling and testing at the time of diagnosis. We examined predictors of genetic testing (GT) in this population. METHODS Within a randomized controlled trial of proactive rapid genetic counseling and testing vs usual care, patients completed a baseline survey within 6 weeks of breast cancer diagnosis but before a definitive survey. We conducted a multinomial logistic regression to identify predictors of GT timing/uptake. RESULTS Having discussed GT with a surgeon was a dominant predictor (χ2 (2, N = 320) = 70.13; P more...

Breast cancer is one of the most common cancers threatening women worldwide. A limited number of available treatment options, frequent recurrence, and drug resistance exacerbate the prognosis of breast cancer patients. Thus, there is an urgent need for methods to investigate novel treatment options, while taking into account the vast molecular heterogeneity of breast cancer. Recent advances in molecular profiling technologies, including genomics, epigenomics, transcriptomics, proteomics and metabolomics data, enable approaching breast cancer biology at multiple levels of omics interaction networks. Systems biology approaches, including computational inference of 'big data' and mechanistic modelling of specific pathways, are emerging to identify potential novel combinations of breast cancer subtype signatures and more diverse targeted therapies. more...

Dermatologic manifestations of inflammatory bowel disease (IBD) are common, and certain IBD medications increase the risk of skin cancer. To define the rates of care and factors associated with dermatologic utilization with a focus on skin cancer screening. We utilized a prospective, natural history IBD research registry to evaluate all outpatient healthcare encounters from 2010 to 2016. Gastrointestinal, dermatologic and primary care visits per individual were identified. We calculated the proportion of patients obtaining care, categorized primary indications for dermatologic visits, determined the incidence of melanoma and non-melanoma skin cancers, and used logistic regression to determine factors associated with dermatology utilization. Of the 2127 IBD patients included, 452 (21.3%) utilized dermatology over the study period, and 55 (2.6%) had a total body skin examination at least once. The 452 patients incurred 1633 dermatology clinic visits, 278 dermatologic procedures, and 1108 dermatology telephone encounters. The most frequent indication was contact dermatitis or dermatitis. Factors associated with dermatology use were family history of skin cancer, employment, systemic steroids, longer disease duration, emergency room use, and the number of IBD-related clinic visits. Between 8.3 and 11% of IBD patients recommended for skin cancer screening visited dermatology each year, and the resulting incidence of non-melanoma skin cancer was 35.4/10,000 [95% CI 23.3–51.5] and melanoma was 6.56/10,000 [95% CI 2.1–15.3]. Less than one in ten IBD patients obtain dermatologic care. Given the increased risk of skin cancers among IBD patients, an emphasis on education, prevention, and screening merits attention. more...

Summary Different models to investigate the prognosis of peripheral T cell lymphoma not otherwise specified (PTCL‐NOS) have been developed by means of retrospective analyses. Here we report on a new model designed on data from the prospective T Cell Project. Twelve covariates collected by the T Cell Project were analysed and a new model (T cell score), based on four covariates (serum albumin, performance status, stage and absolute neutrophil count) that maintained their prognostic value in multiple Cox proportional hazards regression analysis was proposed. Among patients registered in the T Cell Project, 311 PTCL‐NOS were retained for study. At a median follow‐up of 46 months, the median overall survival (OS) and progression‐free survival (PFS) was 20 and 10 months, respectively. Three groups were identified at low risk (LR, 48 patients, 15%, score 0), intermediate risk (IR, 189 patients, 61%, score 1–2), and high risk (HiR, 74 patients, 24%, score 3–4), having a 3‐year OS of 76% [95% confidence interval 61–88], 43% [35–51], and 11% [4–21], respectively (P more...

Crohn’s disease and ulcerative colitis are inflammatory bowel diseases (IBDs) and they primarily involve the intestines and confer an increased risk of thromboembolism (TE). Here we report a case of a young man with active ulcerative colitis (UC) who presented with shortness of breath and syncope. He was found on imaging to have an extensive bilateral pulmonary embolism (PE) and right heart strain with associated pulmonary infarctions. The patient was initially managed with a heparin infusion and subsequently transitioned to a direct acting oral anticoagulant (DOAC) with clinical improvement in his symptoms. more...

PurposeTelegenetics has become the predominant mode of cancer genetic counseling during the COVID-19 pandemic. We sought to identify potential patient-level contraindicators for telegenetic genetic counseling.MethodsWe analyzed post-counseling (pre-result disclosure) follow-up data from a randomized noninferiority trial of a telephone genetic counseling versus usual care genetic counseling. Among 669 randomized participants, 600 completed pre-test counseling and 568 completed a 2-week follow-up assessment before receiving test results. In this analysis, we focused on genetic counseling outcomes (knowledge, decisional conflict, and distress). In multivariate models controlling for bivariate predictors of these outcomes, we tested our a priori hypotheses that pre-counseling numeracy, perceived stress, and race/ethnicity would moderate the outcomes of telephone genetic counseling versus usual care.ResultsOnly numeracy significantly moderated associations between mode of genetic counseling and outcomes. Higher numeracy was associated with higher post-counseling knowledge following telephone genetic counseling ( p 0.20).ConclusionAlthough high numeracy was associated with higher levels of knowledge following telegenetic counseling, we did not identify any clinically significant patient-level contraindicators for telegenetic counseling. These results lend further confidence to the broad use of telegenetics. more...

BACKGROUND Patients with inflammatory bowel disease are at an increased risk of Clostridium difficile infection (CDI), but the impact of CDI on disease severity is unclear. The aim of this study was to determine the effect of CDI on long-term disease outcome in a matched cohort of patients with inflammatory bowel disease. METHODS Patients who tested positive for infection formed the CDI-positive group. We generated a 1:2 propensity matched case to control cohort based on risk factors for CDI in the year before infection. Health care utilization data (emergency department use, hospitalizations, and telephone encounters), medications, laboratories, disease activity, and quality-of-life metrics were compared by CDI status. RESULTS A total of 198 patients (66 CDI and 132 matched controls) were included (56.6% women; 60.1% Crohn's disease, and 39.9% ulcerative colitis). In the year of infection, having CDI was significantly associated with more steroid and antibiotic exposure, elevated C-reactive protein or erythrocyte sedimentation rate, low vitamin D, increased disease activity, worse quality of life, and increased health care utilization (all P < 0.01). During the next year after infection, patients with CDI continued to have increased exposure to CDI-targeted antibiotics (P < 0.001) and other antibiotics (P = 0.02). They also continued to have more clinic visits (P = 0.02), telephone encounters (P = 0.001), and increased health care financial charges (P = 0.001). CONCLUSIONS CDI in inflammatory bowel disease is significantly associated with markers of disease severity, increased health care utilization and poor quality of life during the year of infection, and a 5-fold increase in health care charges in the year after infection (see Video Abstract, Supplemental Digital Content, http://links.lww.com/IBD/B658). more...

Background Mammographic breast density is one of the strongest risk factors for breast cancer after age and family history. Mandatory breast density disclosure policies are increasing nationally without clear guidance on how to communicate density status to women. Coupling density disclosure with personalized risk counseling and decision support through a web-based tool may be an effective way to allow women to make informed, values-consistent risk management decisions without increasing distress. Methods/design This paper describes the design and methods of Engaged, a prospective, randomized controlled trial examining the effect of online personalized risk counseling and decision support on risk management decisions in women with dense breasts and increased breast cancer risk. The trial is embedded in a large integrated health care system in the Pacific Northwest. A total of 1250 female health plan members aged 40–69 with a recent negative screening mammogram who are at increased risk for interval cancer based on their 5-year breast cancer risk and BI-RADS® breast density will be randomly assigned to access either a personalized web-based counseling and decision support tool or standard educational content. Primary outcomes will be assessed using electronic health record data (i.e., chemoprevention and breast MRI utilization) and telephone surveys (i.e., distress) at baseline, six weeks, and twelve months. Discussion Engaged will provide evidence about whether a web-based personalized risk counseling and decision support tool is an effective method for communicating with women about breast density and risk management. An effective intervention could be disseminated with minimal clinical burden to align with density disclosure mandates. Clinical Trials Registration Number: NCT03029286 . more...

Background With increased understanding of the unique entities, subtype-specific approaches for peripheral T-cell lymphoma (PTCL) are emerging, and more precise diagnoses are becoming increasingly important. Patients and Methods We analyzed the approach to the histopathologic diagnosis of PTCL using data from the comprehensive oncology measures of peripheral T-cell lymphoma (COMPLETE) study. The COMPLETE trial is a large prospective cohort study of patients with newly diagnosed PTCL in the United States. Results A total of 499 patients were enrolled from 40 academic and 15 community-based centers. Baseline assessment forms were collected for 493 patients, of which 435 (88%) were available for analysis. The most common diagnoses were PTCL, not otherwise specified (PTCL-NOS), anaplastic large cell lymphoma, and angioimmunoblastic T-cell lymphoma (AITL). A mean of 10 markers (range, 0-21) was assessed per patient. CD30 was assessed frequently but not uniformly in cases that were not anaplastic large cell lymphoma. Only 17% of PTCL-NOS cases were assessed for PD1. CXCL13 was a relatively sensitive marker in AITL, expressed in 84% of tested cases; however, only 3% of PTCL-NOS cases were tested. T follicular helper cell marker assessment differed between academic and community practices, with PD1 more often evaluated by academic centers in cases of AITL (62% vs. 12%; P = .01). Conclusion The diagnostic workup for PTCL in the United States varies widely and often lacks important phenotypic information to fully characterize the lymphoma. Gaps in testing of selected markers should be filled, given the impending revision to the World Health Organization classification. The accuracy of diagnosis will become increasingly important as we enter the era of targeted treatment for PTCL. more...

Introduction We examined patient characteristics, treatments and outcomes of transformed mycosis fungoides (tMF) patients from COMPLETE: a large, multicenter, prospective cohort study of peripheral T-cell lymphoma patients in the US. Methods Patients with tMF were enrolled in COMPLETE at the time of transformation. For this analysis, we identified tMF patients with completed baseline, treatment and follow-up records. Median survival was assessed using Kaplan-Meier methodology. Results Of the 499 patients enrolled in COMPLETE, 17 had tMF. Median age was 61; 53% were male, 9 had elevated lactate dehydrogenase (LDH) and 9 had lymph node involvement. About one-quarter of the patients were African American and 47% had CD30+ disease. Median time to transformation was 53 months. All patients received systemic therapy, with 19% receiving concomitant radiotherapy. Most patients (87%) received single agents, including liposomal doxorubicin, pralatrexate and gemcitabine. Eight patients (50%) had reported responses to therapy. Median survival was 18 months. One- and two-year survival rates were 56% and 44%, respectively. Conclusions tMF often express CD30 and present with lymph-node involvement. Responses have been seen with single agents, but survival remains poor. Novel treatment approaches are urgently needed to improve outcomes. more...

Background Cholecystectomy (CCY) is one of the most frequently performed abdominal surgeries. However, the impact of CCY in clinical settings with altered gastrointestinal physiology and anatomy, such as Crohn’s disease (CD), has not been fully characterized. We sought to investigate clinical outcomes, disease severity, and quality of life of CD patients after CCY. Methods We utilized a prospective, longitudinal registry of consented CD patients followed at a tertiary center. Crohn’s disease patients that had or had not undergone CCY formed the 2 study groups. The absence or presence of gallbladder was confirmed with abdominal CT scans obtained during routine care. Multiyear clinical, biochemical, and histologic data were collected and analyzed. Results Among 834 CD patients, 151 (18%) had undergone CCY. History of CCY was associated with higher disease activity (median Harvey-Bradshaw index; P Conclusions CCY in CD patients was associated with multiple markers of disease activity and worse quality of life during multiyear follow up. This data suggests that CCY in CD patients may adversely impact the long-term clinical course. more...

Cancer is a multifactorial disease, which involves intricate signalling pathways leading to different cellular processes such as survival, proliferation, differentiation or apoptosis. This diversity significantly complicates cancer investigation and treatment. There have been studies on investigating signalling in cancer, but it is difficult to rely solely on molecular biology approaches in order to predict the properties of cancer pathways. Therefore, mathematical modelling has been increasingly used to understand tumour progression, direct the design of new experiments by introducing likely candidates for clinical investigation and present novel approaches to cancer therapy. Different types of modelling techniques, including static and dynamic methods, have been used to model processes that occur in cancer. Boolean models have attracted a large interest in cancer research due to their efficiency and scalability. We here review the use of Boolean modelling for cancer, highlighting the facts that this technique is efficient at generating predictions and that the gain brought by their scalability and flexibility often offsets the lack of quantitative values upon which they are based. more...

Background: Outcomes for patients with peripheral T-cell lymphoma (PTCL) who fail to achieve complete response (CR) or relapse after front-line therapy are poor with lack of prospective outcomes data. Objectives: COMPLETE is a prospective registry of 499 patients enrolled at academic and community sites in the United States detailing patient demographics, treatment and outcomes for patients with aggressive T cell lymphomas. We report results for patients with primary refractory and relapsed disease. Methods: Primary refractory disease was defined as an evaluable best response to initial treatment (induction ± maintenance or consolidation/transplant) other than CR, and included a partial response, progressive disease, or no response/stable disease. Relapsed disease was defined as an evaluable best response to initial treatment of CR, followed by disease progression at a later date, irrespective of time to progression. Patients were included in the analysis if initial treatment began within 30 days of enrollment and treatment duration was ≥4 days. Results: Of 420 evaluable patients, 97 met the definition for primary refractory and 58 with relapsed disease. In the second-line setting, relapsed patients received single-agent therapies more often than refractory patients (52 vs. 28%; p = 0.01) and were more likely to receive single-agent regimens (74 vs. 53%; p = 0.03). The objective response rate to second-line therapy was higher in relapsed patients (61 vs. 40%; p = 0.04) as was the proportion achieving a CR (41 vs. 14%; p = 0.002). Further, relapsed patients had longer overall survival (OS) compared to refractory patients, with a median OS of 29.1 versus 12.3 months. Conclusions: Despite the availability of newer active single agents, refractory patients were less likely to receive these therapies and continue to have inferior outcomes compared to those with relapsed disease. PTCL in the real world remains an unmet medical need, and improvements in front-line therapies are needed. more...

We investigated correlations between histologic features of the colonic mucosa in patients with ulcerative colitis (UC) and clinical outcomes during a 3-year follow-up period.We obtained baseline biopsies from all colorectal segments (n = 889) from 281 patients with UC enrolled in a prospective study at a single center from 2009 through 2013. Biopsies were assessed in a blinded manner using validated histologic scoring systems (the Geboes score, Nancy histopathologic index, and Robarts histopathologic index). Clinical, endoscopic, and histologic data were collected and tested for correlations with systemic corticosteroid use, hospitalization, and colectomy within 3 years of the index colonoscopy.We found histologic evidence of UC activity (Geboes score ≥ 2B.1) in biopsies from 182 patients (65%) and endoscopic evidence of UC activity in 149 patients (53%) (substantial agreement, κ = 0.60). Histologic features of UC activity were associated with increased rates of systemic corticosteroid use, colectomy, and hospitalization in the entire cohort (P.05 for all) and associated with increased rates of systemic corticosteroid use in an analysis limited to patients in endoscopic remission (P.001). In patients in endoscopic remission, only histologic activity was independently associated with use of systemic corticosteroids (multivariate odds ratio, 6.34; 95% CI, 2.20-18.28; P = .001). Similar results were seen when the entire cohort was analyzed. Compared with patients without histologic evidence of UC activity, patients with only a small number of mucosal neutrophils still had higher rates of systemic corticosteroid use (P.001).Histologic evidence of UC activity, including small numbers of neutrophils in the colonic mucosa, is the only factor independently associated with use of systemic corticosteroids. Complete resolution of neutrophil-associated inflammation should be a target for treatment of UC. more...

The development of high-throughput ‘omic techniques has sparked a rising interest in genome-scale metabolic models, with applications ranging from disease diagnostics to crop adaptation. Efficient and accurate methods are required to analyze large metabolic networks. Flux sampling can be used to explore the feasible flux solutions in metabolic networks by generating probability distributions of steady-state reaction fluxes. Unlike other methods, flux sampling can be used without assuming a particular cellular objective. We have undertaken a rigorous comparison of several sampling algorithms and concluded that the coordinate hit-and-run with rounding (CHRR) algorithm is the most efficient based on both run-time and multiple convergence diagnostics. We demonstrate the power of CHRR by using it to study the metabolic changes that underlie photosynthetic acclimation to cold of Arabidopsis thaliana plant leaves. In combination with experimental measurements, we show how the regulated interplay between diurnal starch and organic acid accumulation defines the plant acclimation process. We confirm fumarate accumulation as a requirement for cold acclimation and further predict γ–aminobutyric acid to have a key role in metabolic signaling under cold conditions. These results demonstrate how flux sampling can be used to analyze the feasible flux solutions across changing environmental conditions, whereas eliminating the need to make assumptions which introduce observer bias., Metabolic modeling: flux sampling to study acclimation Flux sampling minimizes observer bias and is therefore a powerful tool for studying metabolic acclimation. Unlike other methods, flux sampling can be used without assuming that metabolism is optimized towards a single objective. This is particularly useful when studying metabolism in changing environments. A team lead by Jean-Marc Schwartz compared three different flux sampling algorithms in order to identify the most appropriate method to analyze changes in metabolic phenotypes. They applied flux sampling to several large-scale networks of plant metabolism to predict metabolic properties across changing temperatures. In order to breed plants for global climate changes, the limits on photosynthesis and metabolism across different environmental conditions need to be understood. Here, they used flux sampling methods to understand changes in photosynthesis and carbon accumulation in cold temperatures. They showed how an intricate balance between carbon and nitrogen metabolism is crucial for acclimation to cold. more...

Background: HER2 (human epidermal growth factor 2)-positive breast cancer is an aggressive type of breast cancer characterized by the overexpression of the receptor-type protein tyrosine kinase HER2 or amplification of the HER2 gene. It is commonly treated by the drug trastuzumab (Herceptin), but resistance to its action frequently develops and limits its therapeutic benefit. Dual-specificity phosphatases (DUSPs) were previously highlighted as central regulators of HER2 signaling, therefore, understanding their role is crucial to designing new strategies to improve the efficacy of Herceptin treatment. We investigated whether inhibiting certain DUSPs re-sensitized Herceptin-resistant breast cancer cells to the drug. We built a series of kinetic models incorporating the key players of HER2 signaling pathways and simulating a range of inhibition intensities. The simulation results were compared to live tumor cells in culture, and showed good agreement with the experimental analyses. In particular, we observed that Herceptin-resistant DUSP16-silenced breast cancer cells became more responsive to the drug when treated for 72 h with Herceptin, showing a decrease in resistance, in agreement with the model predictions. Overall, we showed that the kinetic modeling of signaling pathways is able to generate predictions that assist experimental research in the identification of potential targets for cancer treatment. more...

Plants adjust their photosynthetic capacity in response to their environment in a way that optimizes their yield and fitness. There is growing evidence that this acclimation is a response to changes in the leaf metabolome, but the extent to which these are linked and how this is optimized remain poorly understood. Using as an example the metabolic perturbations occurring in response to cold, we define the different stages required for acclimation, discuss the evidence for a metabolic temperature sensor, and suggest further work towards designing climate-smart crops. In particular, we discuss how constraint-based and kinetic metabolic modelling approaches can be used to generate targeted hypotheses about relevant pathways, and argue that a stronger integration of experimental and in silico studies will help us to understand the tightly regulated interplay of carbon partitioning and resource allocation required for photosynthetic acclimation to different environmental conditions. more...

OBJECTIVE To examine whether health-related stressors and resources are associated with physical function, depression, and anxiety in Chinese American and White breast cancer survivors. METHOD During 2011-2013, this cross-sectional study enrolled Chinese American and White women from California cancer registries diagnosed with Stage 0-III breast cancer between 2006 and 2012. Survivors completed a telephone survey assessing health-related factors including comorbidity, treatment-related symptoms, medical communication, perceived threat, use of coping, and social support resources. Outcomes were assessed using the Patient-Reported Outcome Measurement Information System® (PROMIS®) short forms. Chinese were classified as low- or high-acculturated based on English proficiency, years in the United States, and interview language. Analyses were conducted using Tobit regression models. RESULTS Low-acculturated Chinese (n = 136) had worse physical functioning than Whites (n = 216), controlling for demographics, cancer stage, and time since diagnosis (β = -3.33, p = .01). This disparity was attenuated after adjusting for comorbidity and symptoms (β = -1.63, p = .18). Perceived threat, disengagement coping, and lack of social support were associated with poorer psychological outcomes, regardless of ethnicity. Although low-acculturated Chinese had lower scores on all health-related factors than Whites, the former reported significantly lower level of depression (β = -3.23) and anxiety (β = -5.8) after adjusting for covariates (both p < .05). High-acculturated Chinese (n = 84) did not differ from Whites except that the former had significantly lower anxiety. CONCLUSION Low-acculturated Chinese may benefit from interventions aimed to improve their physical problems. However, despite experiencing greater psychosocial stress, they reported better emotional functioning. Whether Chinese culture shapes this resiliency, or if it is a reporting bias will need further investigation. (PsycINFO Database Record (c) 2019 APA, all rights reserved). more...