bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Neural and Muscular Adaptation Processes During Resistance Training by Fish Protein Ingestions in Older Adults
Authors: Watanabe Kohei , Holobar Aleš , Mita Yukiko , Tomita Aya , Yoshiko Akito , Kouzaki Motoki , Uchida Kenji , Moritani Toshio 
Published: October 2019

Abstract
Assessments of both neural and muscular adaptations during interventions would provide valuable information for developing countermeasures to age-related muscle dysfunctions. We investigated the effect of fish protein ingestion on training-induced neural and muscular adaptations in older adults. Twenty older adults participated 8 weeks of isometric knee extension training intervention. The participants were divided into two groups who took fish protein (n = 10, Alaska pollack protein, APP) or casein (n = 10, CAS). Maximal muscle strength during knee extension, lower extremity muscle mass (body impedance method), and motor unit firing pattern of knee extensor muscle (high-density surface electromyography) were measured before, during, and after the intervention. Muscle strength were significantly increased in both CAS (124.7 ± 5.8%) and APP (117.1 ± 4.4%) after intervention (p &lt; .05), but no significant differences between the groups were observed (p &gt; .05). Significant increases in lower extremity muscle mass from 0 to 8 weeks were demonstrated only for APP (102.0 ± 3.2, p &lt; .05). Greater changes in motor unit firing pattern following intervention were represented in CAS more than in APP. These results suggest that nutritional supplementations could modulate neural and muscular adaptations following resistance training and fish protein ingestion preferentially induces muscular adaptation without the detectable neural adaptation in older adults.
Impact of relebactam-mediated inhibition of Mycobacterium abscessus BlaMab β-lactamase on the in vitro and intracellular efficacy of imipenem
Authors: Le Run Eva , Atze Heiner , Arthur Michel , Mainardi Jean-Luc 
Published: October 2019

AbstractObjectivesImipenem is one of the recommended β-lactams for the treatment of Mycobacterium abscessus pulmonary infections in spite of the production of BlaMab β-lactamase. Avibactam, a second-generation β-lactamase inhibitor, was previously shown to inactivate BlaMab, but its partner drug, ceftazidime, is devoid of any antibacterial activity against M. abscessus. Here, we investigate whether relebactam, a novel second-generation inhibitor developed in combination with imipenem, improves the activity of this carbapenem against M. abscessus.MethodsThe impact of BlaMab inhibition by relebactam was evaluated by determining MICs, time–kill curves and M. abscessus intracellular proliferation in human macrophages. Kinetic parameters for the inhibition of BlaMab by relebactam were determined by spectrophotometry using nitrocefin as the substrate. The data were compared with those obtained with avibactam.ResultsCombination of relebactam (4 mg/L) with β-lactams led to >128- and 2-fold decreases in the MICs of amoxicillin (from >4096 to 32 mg/L) and imipenem (from 8 to 4 mg/L). In vitro, M. abscessus was not killed by the imipenem/relebactam combination. In contrast, relebactam increased the intracellular activity of imipenem, leading to 88% killing. Relebactam and avibactam similarly potentiated the antibacterial activities of β-lactams although BlaMab was inactivated 150-fold less effectively by relebactam than by avibactam.ConclusionsInhibition of BlaMab by relebactam improves the efficacy of imipenem against M. abscessus in macrophages, indicating that the imipenem/relebactam combination should be clinically considered for the treatment of infections due to M. abscessus.
A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients
Authors: Pishvaian Michael J , Blais Edik M , Bender R Joseph , Rao Shruti , Boca Simina M , Chung Vincent , Hendifar Andrew E , Mikhail Sam , Sohal Davendra P S , Pohlmann Paula R , Moore Kathleen N , He Kai , Monk Bradley J , Coleman Robert L , Herzog Thomas J , Halverson David D , DeArbeloa Patricia , Petricoin Emanuel F , Madhavan Subha 
Published: October 2019

AbstractObjectivesScalable informatics solutions that provide molecularly tailored treatment recommendations to clinicians are needed to streamline precision oncology in care settings.Materials and MethodsWe developed a cloud-based virtual molecular tumor board (VMTB) platform that included a knowledgebase, scoring model, rules engine, an asynchronous virtual chat room and a reporting tool that generated a treatment plan for each of the 1725 patients based on their molecular profile, previous treatment history, structured trial eligibility criteria, clinically relevant cancer gene-variant assertions, biomarker-treatment associations, and current treatment guidelines. The VMTB systematically allows clinician users to combine expert-curated data and structured data from clinical charts along with molecular testing data to develop consensus on treatments, especially those that require off-label and clinical trial considerations.ResultsThe VMTB was used as part of the cancer care process for a focused subset of 1725 patients referred by advocacy organizations wherein resultant personalized reports were successfully delivered to treating oncologists. Median turnaround time from data receipt to report delivery decreased from 14 days to 4 days over 4 years while the volume of cases increased nearly 2-fold each year. Using a novel scoring model for ranking therapy options, oncologists chose to implement the VMTB-derived therapies over others, except when pursuing immunotherapy options without molecular support.DiscussionVMTBs will play an increasingly critical role in precision oncology as the compendium of biomarkers and associated therapy options available to a patient continues to expand.ConclusionFurther development of such clinical augmentation tools that systematically combine patient-derived molecular data, real-world evidence from electronic health records and expert curated knowledgebases on biomarkers with computational tools for ranking best treatments can support care pathways at point of care.
Idiosyncrasies in cities: evaluating patterns and drivers of ant biodiversity along urbanization gradients
Authors: Perez Abe , Diamond Sarah E 
Published: October 2019

Abstract
Urbanization is expected to reduce biodiversity. However, an increasing number of studies report urban biodiversity comparable to that of surrounding nonurban areas, leaving open the question: what maintains biodiversity in cities? We characterized patterns of ant biodiversity across urbanization gradients of three major cities in the Midwestern United States and evaluated the support for two mechanisms underlying the maintenance of biodiversity in cities, specifically via introduced non-native species and differential phenology of communities along each urbanization gradient. We observed idiosyncrasies in ant species diversity such that each city displayed either increased, decreased or no change in biodiversity across the urbanization gradient. We found partial support (one of the three cities) for the hypothesis that non-native species can contribute positively to overall species diversity in cities, though even with introduced species removed from consideration, native ant biodiversity was maintained along the urbanization gradient. We found no support for systematic differential phenology across urbanization gradients, although species diversity did vary over time across all sites. Our results further challenge the assumption of biodiversity loss in cities, as two of our three cities exhibited maintained species diversity along the urbanization gradient. Most importantly, our study demonstrates that urban biodiversity can be maintained entirely by native communities.
Kerosene Nights: Light and Enlightenment in Late Ottoman Jerusalem*
Authors: Wishnitzer Avner 
Published: October 2019

Abstract:
Street lighting was first introduced into Ottoman cities in the second half of the nineteenth century. However, unlike in larger Ottoman cities, where coal gas was used, in Jerusalem it was kerosene that served as burning material, creating the distinct nocturnal reality that is here called the ‘kerosene night’. This reality was the result and, simultaneously, one of the most glaring manifestations of Jerusalem’s economic, administrative and infrastructural peripherality. Between the early 1890s and the First World War, kerosene allowed the Jerusalem municipality an affordable means to respond to inhabitants’ expectations for more light. Both public expectations and municipal action were fanned by a discourse that associated street lighting with Enlightenment, order and progress. Yet, kerosene illumination also set the limits of nocturnal conviviality and frustrated the very expectations it kindled. Measured against larger metropoles, the relative darkness of Jerusalem heightened among residents feelings of provinciality and governmental neglect — feelings that the kerosene lamps, paradoxically, brought to light.
The Infant Cuddler Study: Evaluating the effectiveness of volunteer cuddling in infants with neonatal abstinence syndrome
Authors: Hignell Amanda , Carlyle Karen , Bishop Catherine , Murphy Mary , Valenzano Teresa , Turner Suzanne , Sgro Michael 
Published: October 2019

Abstract

Objectives
St. Michael’s Hospital launched a volunteer cuddling program for all infants admitted into the neonatal intensive care unit in October 2015. The program utilizes trained volunteers to cuddle infants when caregivers are not available. This was a pilot study to assess the impact of a volunteer cuddle program on length of stay (LOS) and feasibility of implementation of the program.

Methods
A mixed methods approach was utilized to measure both quantitative and qualitative impact. A pilot cohort study with a retrospective control group assessed the feasibility of implementing a volunteer cuddling program for infants with neonatal abstinence syndrome (NAS). Length of stay was used as a surrogate marker to measure the impact of cuddling on infants being treated for Neonatal Abstinence Syndrome. Focus groups using semi-structured interviews were conducted with volunteers and nurses at the end of the pilot study.

Results
LOS was reduced by 6.36 days (U=34, P=0.072) for infants with NAS in the volunteer cuddling program. Focus groups with both bedside nurses and program volunteers described a positive impact of cuddling programs on infants, families, staff, and volunteers alike.

Conclusions
The study results suggest that the volunteer cuddling program may reduce LOS in infants with NAS and have potential economic savings on hospital resources. However, larger prospective cohort studies are needed to confirm these results.
In situ sol-gel synthesis of hyaluronan derivatives bio-nanocomposite hydrogels
Authors: D’Amora U , Ronca A , Raucci M G , Dozio S M , Lin H , Fan Y , Zhang X , Ambrosio L 
Published: October 2019

Abstract
The main driving idea of the present study was the comparison between two different chemical modifications of hyaluronic acid (HA) followed by the development of nanocomposite hydrogels directly in situ by biomineralization of photocrosslinkable HA polymers through sol-gel synthesis. In this way, it has been possible to overcome some limitations due to classical approaches based on the physical blending of inorganic fillers into polymer matrix. To this aim, methacrylated and maleated HA, synthesized with similar degree of substitution (DS) were compared in terms of mechanical and physico-chemical properties. The success of in situ biomineralization was highlighted by reflect Fourier transform infrared spectroscopy and thermogravimetric analysis. Furthermore, mechanical characterization demonstrated the reinforcing effect of inorganic fillers evidencing a strong correlation with DS. The swelling behavior resulted to be correlated with filler concentration. Finally, the cytotoxicity tests revealed the absence of toxic components and an increase of cell proliferation over culture time was observed, highlighting these bio-nanocomposite hyaluronan derivatives as biocompatible hydrogel with tunable properties.
Physician Behavior Change: A Systematic Review
Authors: Cunningham Brian P. , Bakker Caitlin J. , Parikh Harsh R. , Johal Herman , Swiontkowski Marc F. 
Published: October 2019

Summary:
Evidence-based medicine (EBM) has been advocated as one of the central dogmas of health care since the late 20th century. EBM provides health care entities the prospect to revolutionize health care practices and improve the standard of health care for everyone. Therefore, the potential benefits for adopting EBM practices cannot be overlooked. However, physicians face an increasingly difficult challenge, both personal and professional, when adopting EBM practices. Therefore, knowledge of effective strategies for driving physician behavioral is necessary. To this effort, this systematic review is tasked to compile and analyze the literature focused on physician behavior change. After a review of 1970 studies, 29 different studies were meticulously evaluated by 2 separate reviewers. Studies were then categorized into 5 broad distinctions based on their assessed outcomes: (1) physician knowledge; (2) ordering of tests; (3) compliance with protocols; (4) prescription of medications; and (5) complication rates. The testing group was focused on osteoporosis screening, using educational interventions. Protocol compliance studies were heterogeneous, ranging from diagnosing supracondylar fractures in pediatric patients to antimicrobial administration. Prescription pattern studies were primarily focused around the management of osteoporosis. Multimodal interventions seemed to be more effective when producing change. However, due to the variability in intervention type and outcomes assessment, it is difficult to conclude the most effective intervention for driving physician behavioral change. Physician behavior and specifically surgeon behavior are disproportionately influenced by mentors, fellowship training, and memories of excellent or catastrophic outcomes much more so than literature and data. Adopting evidence-based practices (EBM) and value centric care may provide an opportunity for physicians to improve personal performance.
ClustR: A Space–Time Cluster Analysis R Package for Individual-level Data
Authors: Enders Catherine , Hyde Rebecca J. , Selvin Steve , Metayer Catherine , Francis Stephen Starko 
Published: October 2019

Background:Until recently, large individual-level longitudinal data were unavailable to investigate clusters of disease, driving a need for suitable statistical tools. We introduce a robust, efficient, intuitive R package, ClustR, for space–time cluster analysis of individual-level data.Methods:We developed ClustR and evaluated the tool using a simulated dataset mirroring the population of California with constructed clusters. We assessed Cluster’s performance under various conditions and compared it with another space–time clustering algorithm: SaTScan.Results:ClustR mostly exhibited high sensitivity for urban clusters and low sensitivity for rural clusters. Specificity was generally high. Compared with SaTScan, ClustR ran faster and demonstrated similar sensitivity, but had lower specificity. Select cluster types were detected better by ClustR than SaTScan and vice versa.Conclusion:ClustR is a user-friendly, publicly available tool designed to perform efficient cluster analysis on individual-level data, filling a gap among current tools. ClustR and SaTScan exhibited different strengths and may be useful in conjunction.
Human Reference Genome and a High Contiguity Ethnic Genome AK1
Authors: Kim Jina , Sung Joohon , Han Kyudong , Lee Wooseok , Mun Seyoung , Lee Jooyeon , Bahk Kunhyung , Yang Inchul , Bae Young-Kyung , Kim Changhoon , Kim Jong-il , Seo Jeongsun 
Published: October 2019

AbstractStudies have shown that the current human reference genome (GRCh38) might miss information for some populations, but “exactly what we miss” is still elusive due to the lower contiguity of non-reference genomes. We juxtaposed the GRCh38 with high contiguity genome assemblies, AK1, to show that ∼1.8% (∼53.4 Mbp) of AK1 sequences missed in GRCh38 with ∼0.76% (∼22.2 Mbp) of ectopic chromosomes. The unique AK1 sequences harbored ∼1,390 putative coding elements. We found that ∼5.3Mb (∼0.2%) of the AK1 sequences aligned and recovered the “unmapped” reads of fourteen individuals (5 East-Asians, 4 Europeans, and 5 Africans) as a reference. The regions that “unmapped” reads aligned included 110 common (shared between ≥2 individuals) and 38 globally (≥7 individuals) missing regions with 25 candidate coding elements. We verified that many of the common missing regions exist in multiple populations and chimpanzee’s DNA. Our study illuminates not only the discovery of missing information but the use of highly precise ethnic genomes in understanding human genetics.
Rapid and differential evolution of the venom composition of a parasitoid wasp depending on the host strain
Authors: Cavigliasso Fanny , Mathé-Hubert Hugo , Kremmer Laurent , Rebuf Christian , Gatti Jean-Luc , Malausa Thibaut , Colinet Dominique , Poirié Marylène 
Published: October 2019

AbstractParasitoid wasps rely primarily on venom to suppress the immune response and regulate the physiology of their host. Intraspecific variability of venom protein composition has been documented in some species, but its evolutionary potential is poorly understood. We performed an experimental evolution initiated with crosses of two lines ofLeptopilina boulardiof different venom composition to generate variability and create new combinations of venom factors. The offspring were maintained for 10 generations on two strains ofDrosophila melanogasterdiffering in resistance / susceptibility to the parasitoid lines. The venom composition of individuals was characterized by a semi-automatic analysis of 1D SDS-PAGE protein profiles whose accuracy was checked by Western blot analysis of well-characterized venom proteins. Results evidenced a rapid and differential evolution of the venom composition on both hosts and showed that the proteins beneficial on one host can be costly on the other. Overall, we demonstrated the capacity of rapid evolution of the venom composition in parasitoid wasps, important regulators of arthropod populations, suggesting a potential for adaptation to new hosts. Our approach also proved relevant in identifying, among the diversity of venom proteins, those possibly involved in parasitism success and whose role deserves to be deepened.Key ContributionThe venom protein composition of parasitoid wasps can evolve rapidly and differently depending on the host strain. Studying this evolution can help identify new venom proteins possibly involved in parasitism success on a given host.
Phosphoregulation provides functional specificity to biomolecular condensates in the cell cycle and cell polarity
Authors: Gerbich Therese M. , Gladfelter Amy S. 
Published: October 2019

AbstractCytoplasmic patterning is a feature of many cells from embryos to neurons and fungi. Biomolecular condensation is a way of organizing cytosol in which proteins and nucleic acids coassemble into compartments. How molecular identity of condensates is achieved is not well understood. In the multinucleate, filamentous fungus Ashbya gossypii, the RNA-binding protein Whi3 regulates the cell cycle and cell polarity through forming macromolecular structures that behave like condensates. Whi3 has distinct spatial localizations and mRNA targets making it a powerful model for how, when and where specific identities are established for condensates. Using mass-spectrometry, we identified residues on Whi3 that are differentially phosphorylated under specific conditions and generated mutants which ablate this regulation. This yielded separation of function alleles that were functional for either cell polarity or nuclear cycling but not both. This study shows that phosphorylation of individual residues on molecules in biomolecular condensates can provide specificity that give rise to distinct functional identities in the same cell.SummaryResidue specific phosphorylation of the RNA-binding protein Whi3 is used to specifically regulate subsets of functionally distinct condensates in the multinucleate fungus Ashbya gossypii.
Selecting for altered substrate specificity reveals the evolutionary flexibility of ATP-binding cassette transporters
Authors: Srikant Sriram , Gaudet Rachelle , Murray Andrew W. 
Published: October 2019

AbstractABC transporters are the largest family of ATP-hydrolyzing transporters, with members in every sequenced genome, which transport substrates across membranes. Structural studies and biochemistry highlight the contrast between the global structural similarity of homologous transporters and the enormous diversity of their substrates. How do ABC transporters evolve to carry such diverse molecules and what variations in their amino acid sequence alter their substrate selectivity? We mutagenized the transmembrane domains of a conserved fungal ABC transporter that exports a mating pheromone and selected for mutants that export a non-cognate pheromone. Mutations that alter export selectivity cover a region that is larger than expected for a localized substrate-binding site. Individual selected clones have multiple mutations which have broadly additive contributions to specific transport activity. Our results suggest that multiple positions influence substrate selectivity, leading to alternative evolutionary paths towards selectivity for particular substrates, and explaining the number and diversity of ABC transporters.
BATCAVE: Calling somatic mutations with a tumor- and site-specific prior
Authors: Mannakee Brian K. , Gutenkunst Ryan N. 
Published: October 2019

AbstractDetecting somatic mutations withins tumors is key to understanding treatment resistance, patient prognosis, and tumor evolution. Mutations at low allelic frequency, those present in only a small portion of tumor cells, are particularly difficult to detect. Many algorithms have been developed to detect such mutations, but none models a key aspect of tumor biology. Namely, every tumor has its own profile of mutation types that it tends to generate. We present BATCAVE (Bayesian Analysis Tools for Context-Aware Variant Evaluation), an algorithm that first learns the individual tumor mutational profile and mutation rate then uses them in a prior for evaluating potential mutations. We also present an R implementation of the algorithm, built on the popular caller MuTect. Using simulations, we show that adding the BATCAVE algorithm to MuTect improves variant detection. It also improves the calibration of posterior probabilities, enabling more principled tradeoff between precision and recall. We also show that BATCAVE performs well on real data. Our implementation is computationally inexpensive and straightforward to incorporate into existing MuTect pipelines. More broadly, the algorithm can be added to other variant callers, and it can be extended to include additional biological features that affect mutation generation.