nils-herrmann/clean_scirepeval huggingface dataset:
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
Venue: Nucleic Acids Res.

The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http:/consurf.tau.ac.il) established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain) mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub tree.
Radiomic Profiling of Glioblastoma: Identifying an Imaging Predictor of Patient Survival with Improved Performance over Established Clinical and Radiologic Risk Models.
Venue: Radiology

To evaluate whether radiomic feature based magnetic resonance (MR) imaging signatures allow prediction of survival and stratification of patients with newly diagnosed glioblastoma with improved accuracy compared with that of established clinical and radiologic risk models.  Retrospective evaluation of data was approved by the local ethics committee and informed consent was waived. A total of 119 patients (allocated in a 2:1 ratio to a discovery [n 79] or validation [n 40] set) with newly diagnosed glioblastoma were subjected to radiomic feature extraction (12 190 features extracted, including first order, volume, shape, and texture features) from the multiparametric (contrast material enhanced T1 weighted and fluid attenuated inversion recovery imaging sequences) and multiregional (contrast enhanced and unenhanced) tumor volumes. Radiomic features of patients in the discovery set were subjected to a supervised principal component (SPC) analysis to predict progression free survival (PFS) and overall survival (OS) and were validated in the validation set. The performance of a Cox proportional hazards model with the SPC analysis predictor was assessed with C index and integrated Brier scores (IBS, lower scores indicating higher accuracy) and compared with Cox models based on clinical (age and Karnofsky performance score) and radiologic (Gaussian normalized relative cerebral blood volume and apparent diffusion coefficient) parameters.  SPC analysis allowed stratification based on 11 features of patients in the discovery set into a low or high risk group for PFS (hazard ratio [HR] 2.43; P .002) and OS (HR, 4.33; P .001) and the results were validated successfully in the validation set for PFS (HR, 2.28; P .032) and OS (HR, 3.45; P .004) The performance of the SPC analysis (OS: IBS, 0.149; C index, 0.654; PFS: IBS, 0.138; C index, 0.611) was higher compared with that of the radiologic (OS: IBS, 0.175; C index, 0.603; PFS: IBS, 0.149; C index, 0.554) and clinical risk models (OS: IBS, 0.161, C index, 0.640; PFS: IBS, 0.139; C index, 0.599) The performance of the SPC analysis model was further improved when combined with clinical data (OS: IBS, 0.142; C index, 0.696; PFS: IBS, 0.132; C index, 0.637)  An 11 feature radiomic signature that allows prediction of survival and stratification of patients with newly diagnosed glioblastoma was identified, and improved performance compared with that of established clinical and radiologic risk models was demonstrated. (c) RSNA, 2016 Online supplemental material is available for this article.
Improved Risk Assessment by Integrating Molecular and Clinicopathological Factors in Early stage Endometrial Cancer Combined Analysis of the PORTEC Cohorts
Venue: Clinical Cancer Research

Recommendations for adjuvant treatment for women with early stage endometrial carcinoma are based on clinicopathologic features. Comprehensive genomic characterization defined four subgroups: p53 mutant, microsatellite instability (MSI) POLE mutant, and no specific molecular profile (NSMP) We aimed to confirm the prognostic capacity of these subgroups in large randomized trial populations, investigate potential other prognostic classifiers, and integrate these into an integrated molecular risk assessment guiding adjuvant therapy.  Analysis of MSI, hotspot mutations in 14 genes including POLE, protein expression of p53, ARID1a, b catenin, L1CAM, PTEN, ER, and PR was undertaken on 947 available early stage endometrioid endometrial carcinomas from the PORTEC 1 and 2 trials, mostly high intermediate risk (n 614) Prognostic value was determined using univariable and multivariable Cox proportional hazard models. AUCs of different risk stratification models were compared.  Molecular analyses were feasible in >96% of the patients and confirmed the four molecular subgroups: p53 mutant (9% MSI (26% POLE mutant (6% and NSMP (59% Integration of prognostic molecular alterations with established clinicopathologic factors resulted in a stronger model with improved risk prognostication. Approximately 15% of high intermediate risk patients had unfavorable features (substantial lymphovascular space invasion, p53 mutant, and/or >10% L1CAM) 50% favorable features (POLE mutant, NSMP being microsatellite stable, and CTNNB1 wild type) and 35% intermediate features (MSI or CTNNB1 mutant)  Integrating clinicopathologic and molecular factors improves the risk assessment of patients with early stage endometrial carcinoma. Assessment of this integrated risk profile is feasible in daily practice, and holds promise to reduce both overtreatment and undertreatment.
Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta
Venue: Proteins

We describe CASP11 de novo blind structure predictions made using the Rosetta structure prediction methodology with both automatic and human assisted protocols. Model accuracy was generally improved using coevolution derived residue residue contact information as restraints during Rosetta conformational sampling and refinement, particularly when the number of sequences in the family was more than three times the length of the protein. The highlight was the human assisted prediction of T0806, a large and topologically complex target with no homologs of known structure, which had unprecedented accuracy <3.0 A root mean square deviation (RMSD) from the crystal structure over 223 residues. For this target, we increased the amount of conformational sampling over our fully automated method by employing an iterative hybridization protocol. Our results clearly demonstrate, in a blind prediction scenario, that coevolution derived contacts can considerably increase the accuracy of template free structure modeling. Proteins 2016; 84(Suppl 1):67 75.
Improved Efficacy of Neoadjuvant Compared to Adjuvant Immunotherapy to Eradicate Metastatic Disease.
Venue: Cancer discovery

Immunotherapy has recently entered a renaissance phase with the approval of multiple agents for the treatment of cancer. Immunotherapy stands ready to join traditional modalities, including surgery, chemotherapy, radiation, and hormone therapy, as a pillar of cancer treatment. Although immunotherapy has begun to have success in advanced cancer treatment, its scheduling and efficacy with surgery to treat earlier stages of cancer and prevent distant metastases have not been systematically examined. Here, we have used two models of spontaneously metastatic breast cancers in mice to illustrate the significantly greater therapeutic power of neoadjuvant, compared with adjuvant, immunotherapies in the context of primary tumor resection. Elevated and sustained peripheral tumor specific immune responses underpinned the outcome, and blood sampling of tumor specific CD8+ T cells immediately prior to and post surgery may provide a predictor of outcome. These data now provide a strong rationale to extensively test and compare neoadjuvant immunotherapy in humans.  We demonstrate the significantly greater therapeutic efficacy of neoadjuvant, compared with adjuvant, immunotherapies to eradicate distant metastases following primary tumor resection. Elevated and sustained peripheral tumor specific immune responses underpinned the outcome, and blood sampling of tumor specific CD8+ T cells immediately prior to and post surgery may provide a predictor of outcome. Cancer Discov; 6(12) 1382 99. (c)2016 AACR.See related commentary by Melero et al. p. 1312This article is highlighted in the In This Issue feature, p. 1293.
An improved representation of geographically isolated wetlands in a watershed scale hydrologic model

Geographically isolated wetlands (GIWs) defined as wetlands surrounded by uplands, provide an array of ecosystem goods and services. Within the United States, federal regulatory protections for GIWs are contingent, in part, on the quantification of their singular or aggregate effects on the hydrological, biological, or chemical integrity of waterways regulated by the Clean Water Act (CWA) However, limited tools are available to assess the downgradient effects of GIWs. We constructed a Soil and Water Assessment Tool (SWAT) model with improved representations of GIW hydrologic processes for the approximately 1700 km2 Pipestem Creek watershed in the Prairie Pothole Region of North Dakota, USA. We then executed a series of novel modifications on the Pipestem Creek SWAT model. We (1) redefined the model's hydrologic response unit spatial boundaries to conform to mapped GIWs and associated watershed boundaries, (2) constructed a series of new model input files to direct the simulation of GIW fill spill hydrology and upland flows to GIWs, and (3) modified the model source code to facilitate use of the new SWAT input files and improve GIW water balance simulations. We then calibrated and verified our modified SWAT model at a daily time step from 2009 through 2013. Simulation results indicated good predictive power (the maximum Nash Sutcliffe Efficiency statistic was 0.86) and an acceptable range of uncertainty (measured using the Sequential Uncertainty Fitting v.2 uncertainty statistics) Simulation results additionally indicated good model performance with respect to GIW water balance simulations based on literature based descriptions of regional GIW hydrologic behaviour. Our modified SWAT model represents a critical step in advancing scientific understandings of the watershed scale hydrologic effects of GIWs and provides a novel method for future assessments in different watersheds and physiographic regions.
Hybrid poly(lactic acid)/nanocellulose/nanoclay composites with synergistically enhanced barrier properties and improved thermomechanical resistance

barrier properties and improved thermomechanical resistance DTU Orbit (10/03/2019) Hybrid poly(lactic acid)/nanocellulose/nanoclay composites with synergistically enhanced barrier properties and improved thermomechanical resistance Poly(lactic acid) (PLA) based hybrid nanocomposites (PLA, nanoclay and nanocellulose) were prepared by reinforcing neat PLA with commercially available nanoclay (Cloisite C30B) and nanocellulose, in the form of either partially acetylated cellulose nanofibres (CNFs) or nanocrystalline cellulose. Composites with 1 or 5 wt% of nanocellulose, in combination with 1, 3 and 5 wt% of nanoclay, were prepared, and their barrier properties were investigated. It was found that the combination of clay and nanocellulose clearly resulted in synergistic behaviour in terms of the oxygen transmission rate (OTR) through a reduction of up to 90% in OTR and a further reduction in the water vapour transmission rate of up to 76% In addition, the nanocomposite films showed improved thermomechanical resistance and improved crystallisation kinetics while maintaining high film transparency. This makes the hybrid PLA/CNF/C30B nanocomposites a very promising material for food packaging applications.
Relationship among quality of nurses' work life, organizational culture and Turnover Intention at Assiut University Hospital

Nurses are amongst the employees whose lives are fully affected by the quality of work life (QWL) as a consequence of dynamic changes in work environment. The aim was to investigate the relationship among nurses' quality of work life, organizational culture and turnover intention at Assiut University Hospital.  A correlational descriptive design was used.  four Intensive Care Units classified as follows: Causality Intensive Care Unit, General Postoperative ICUs, and Coronary Care Unit ( Included all nurses working in aforementioned settings with a total number of 120 nurses. Four tools were used to collect data namely: socio demographic data sheet, quality of nurses' work life, organizational culture questionnaire, and turnover intention questionnaire.  illustrated that nurses' quality of work life scores was highly significant in relation to the department, marital status, organizational culture score, and turnover intention score.  This study contributed to understanding the relationships between quality of nurses work life and organizational culture that will lead to turnover intention among the study sample of hospital nurses and found a positive correlation between quality of nurses work life and organizational culture with highly statistically significant relation and between quality of nurses work life and turnover intention While, there was a negative correlation between turnover intention and organizational culture.  Workshops on the quality of work life skills for nurses and nurse managers should be done periodically. In order to lessen intent to turnover for the nursing profession, staff nurses are encouraged to participate in nursing committees, assume leadership roles, and become decision makers.
Breastfeeding, Bed Sharing, and Maternal Cortisol
Venue: Clinical pediatrics

Prior studies have found that close mother child sleep proximity helps increase rates of breastfeeding, and breastfeeding itself is linked to better maternal and infant health. In this study, we examine whether breastfeeding and infant bed sharing are related to daily rhythms of the stress responsive hormone cortisol. We found that bed sharing was related to flatter diurnal cortisol slopes, and there was a marginal effect for breastfeeding to predict steeper cortisol slopes. Furthermore, mothers who breastfeed but do not bed share had the steepest diurnal cortisol slopes, whereas mothers who bed shared and did not breastfeed had the flattest slopes (P .05) These results were significant after controlling for subjective sleep quality, perceived stress, depression, socioeconomic status, race, and maternal age. Findings from this study indicate that infant parenting choices recommended for infants (breastfeeding and separate sleep surfaces for babies) may also be associated with more optimal stress hormone profiles for mothers.
Determining Player Skill in the Game of Go with Deep Neural Networks
Venue: TPNC

The game of Go has recently been an exuberant topic for AI research, mainly due to advances in Go playing software. Here, we present an application of deep neural networks aiming to improve the experience of humans playing the game of Go online. We have trained a deep convolutional network on 188,700 Go game records to classify players into three categories based on their skill. The method has a very good accuracy of 71.5 when classifying the skill from a single position, and 77.9 when aggregating predictions from one game. The performance and low amount of information needed allow for a much faster convergence to true rank on online Go servers, improving user experience for new coming players. The method will be experimentally deployed on the Online Go Server (OGS)
Menstruation Related Hypersomnia Treated with Hormonal Contraception: Case Report and Review of Literature.
Venue: Puerto Rico health sciences journal

Menstrual related hypersomnia (MRH) is a rare disorder consisting of recurrent hypersomnia that is temporally linked with menses. An unusual case of an 18 yearold female with repeated episodes of hypersomnia was referred to a psychiatrist and a neurologist. A review of the literature was done so that an accurate diagnosis could be made, thereby enabling the development of an appropriate treatment plan. Making an effective diagnosis was a challenge because of the similarity of the symptoms of MRH with other psychiatric disorders. As additional clinical features were identified and treatments were ruled ineffective, further diagnoses were proposed. The patient's symptoms ceased with oral contraceptive treatment. Hormones play a role in the menstrual cycle and frequently affect behavior (such as sleep patterns) This case underlines the importance of multidisciplinary evaluation and treatment in unusual cases. The potential role of hormone fluctuation in patients with psychiatric conditions should be considered when diagnosing and treating those who are unresponsive to traditional pharmacological treatments.
Genome Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development[OPEN]
Venue: Plant Cell

Maize histone deacetylase HDA101 mainly targets active genes regulating H4K5 acetylation and represses a small subset of targets whose expression must be kept at a low level during seed development. Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3 like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101 mediated regulation of transcriptionally active and inactive genes.
OPTIMAL HARVESTING IN DIFFUSIVE POPULATION MODELS WITH SIZE RANDOM GROWTH AND DISTRIBUTED RECRUITMENT

In this article, we consider an optimal harvesting control problem for a spatial diffusion population system, which incorporates individual's random growth of size and distributed style of recruitment. The existence and uniqueness of nonnegative solutions to this practical model is established by means of Banach's fixed point theorem. The continuous dependence of population density on the harvesting effort is analyzed. The optimal harvesting strategies are discussed through normal cone and adjoint techniques. Some conditions are presented to assure that there is only one optimal policy.
Addition of Liposome Bupivacaine to Bupivacaine HCl Versus Bupivacaine HCl Alone for Interscalene Brachial Plexus Block in Patients Having Major Shoulder Surgery
Venue: Regional Anesthesia Pain Medicine

We examined whether liposome bupivacaine (Exparel) given in the interscalene brachial plexus block lowers pain in the setting of multimodal postoperative pain management for major shoulder surgery.  Fifty two adult patients were randomized to receive either 5 mL of 0.25% bupivacaine HCl immediately followed by 10 mL of liposome bupivacaine 133 mg (n 26) or 15 mL of 0.25% standard bupivacaine alone (n 26) in interscalene brachial plexus block. The primary outcome (worst pain in the first postoperative week) was assessed by the Modified Brief Pain Inventory short form. Secondary outcomes were overall satisfaction with analgesia (OBAS) functionality of the surgical arm, sleep duration, time to first opioid (tramadol) request and opioid consumption (mEq) sensory motor block characteristics, and the occurrence of adverse effects.  Worst pain was lower in patients given liposome bupivacaine added to standard bupivacaine than in patients given standard bupivacaine alone (generalized estimating equation [GEE] estimated marginal mean values, 3.6 0.3 vs 5.3 0.4 points on the Numeric Rating Scale, respectively, although the effect was modest, 1.6 0.5; 95% confidence interval, 0.8 2.5) Total OBAS scores indicated greater satisfaction (GEE estimated marginal mean values, 1.8 0.3 vs 3.3 0.4 on total OBAS, respectively, with modest effect, difference, 1.4 0.5; 95% confidence interval, 0.5 2.4) There were no differences in any of the other secondary outcomes.  Liposome bupivacaine added to standard bupivacaine may lower pain and enhance patient's satisfaction in the first postoperative week even in the setting of multimodal analgesia for major shoulder surgery.