bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elbow Flexion Reconstruction in Brachial Plexus Avulsion Injuries – Results with Intercostal Nerve and Distal Nerve Transfers
Authors: Kang Gavrielle Hui-Ying , Lim Rebecca Qian-Ru , Yong Fok-Chuan 
Published: July 2020

Background: The neural surgical options for reconstruction of elbow flexion in brachial plexus injuries depend on the availability of nerve donors. In upper-type avulsion injuries, the ulnar or median nerves, when intact, are reliable intra-plexal donor nerves for transfers to the biceps muscle. In complete avulsion injuries, donors are limited to extra-plexal sources, such as intercostal nerves (ICNs).Methods: We reviewed our results of ICN and partial distal nerve (ulnar or median) transfers for elbow flexion reconstruction in patients with brachial plexus avulsion injuries. The time taken for recovery of elbow flexion strength to M3 and the final motor outcome at 2 years were compared between both groups.Results: 38 patients were included in this study. 27 had ICN transfers to the musculocutaneous nerve (MCN), 8 had partial ulnar nerve transfers and 3 had partial median nerve transfers to the MCN's biceps motor branch. The mean time interval from injury to surgery was 3.6 months. Recovery of elbow flexion was observed earlier in the distal nerve transfer group (p < 0.05). Overall, success rates were higher in patients with distal nerve transfers (100%), compared to ICN transfers (63%) at 2 years (p = 0.018). Patients with distal nerve transfers achieved a higher final median strength of M4.0 [Interquartile range (IQR) 3.5–4.5], compared to M3.5 (IQR 2.0–4.0) in the ICN group (p = 0.031). In the subgroup of patients with upper-type brachial plexus injuries, there were no significant differences in motor outcomes between the ICN versus distal nerve transfers group.Conclusions: In our entire cohort, patients with distal nerve transfers had faster motor recovery and better elbow flexion power than patients with ICN transfers. In patients with partial brachial plexus injuries, outcomes of ICN transfers were not inferior to distal nerve transfers.
Linking Environmental Exposures to Molecular Pathogenesis in Non-Hodgkin Lymphoma Subtypes
Authors: Moubadder Leah , McCullough Lauren E. , Flowers Christopher R. , Koff Jean L. 
Published: July 2020

Abstract
Non-Hodgkin lymphoma comprises a heterogeneous group of hematologic malignancies, with about 60 subtypes that arise via various pathogenetic mechanisms. Although establishing etiology for specific NHL subtypes has been historically difficult given their relative rarity, environmental exposures have been repeatedly implicated as risk factors across many subtypes. Large-scale epidemiologic investigations have pinpointed chemical exposures in particular, but causality has not been established, and the exact biologic mechanisms underpinning these associations are unclear. Here we review chemical exposures that have been associated with development of NHL subtypes and discuss their biologic plausibility based on current research.
Tipifarnib as a Precision Therapy for HRAS-Mutant Head and Neck Squamous Cell Carcinomas
Authors: Gilardi Mara , Wang Zhiyong , Proietto Marco , Chillà Anastasia , Calleja-Valera Juan Luis , Goto Yusuke , Vanoni Marco , Janes Matthew R. , Mikulski Zbigniew , Gualberto Antonio , Molinolo Alfredo A. , Ferrara Napoleone , Gutkind J. Silvio , Burrows Francis 
Published: July 2020

Abstract
Tipifarnib is a potent and highly selective inhibitor of farnesyltransferase (FTase). FTase catalyzes the posttranslational attachment of farnesyl groups to signaling proteins that are required for localization to cell membranes. Although all RAS isoforms are FTase substrates, only HRAS is exclusively dependent upon farnesylation, raising the possibility that HRAS-mutant tumors might be susceptible to tipifarnib-mediated inhibition of FTase. Here, we report the characterization of tipifarnib activity in a wide panel of HRAS-mutant and wild-type head and neck squamous cell carcinoma (HNSCC) xenograft models. Tipifarnib treatment displaced both mutant and wild-type HRAS from membranes but only inhibited proliferation, survival, and spheroid formation of HRAS-mutant cells. In vivo, tipifarnib treatment induced tumor stasis or regression in all six HRAS-mutant xenografts tested but displayed no activity in six HRAS wild-type patient-derived xenograft (PDX) models. Mechanistically, drug treatment resulted in the reduction of MAPK pathway signaling, inhibition of proliferation, induction of apoptosis, and robust abrogation of neovascularization, apparently via effects on both tumor cells and endothelial cells. Bioinformatics and quantitative image analysis further revealed that FTase inhibition induces progressive squamous cell differentiation in tipifarnib-treated HNSCC PDXs. These preclinical findings support that HRAS represents a druggable oncogene in HNSCC through FTase inhibition by tipifarnib, thereby identifying a precision therapeutic option for HNSCCs harboring HRAS mutations.
The Effect of Home Country Natural Disasters on the Academic Outcomes of Immigrant Students in New York City
Authors: Laurito Agustina 
Published: July 2020

Abstract
This paper estimates the impact of home country natural disasters on the academic performance of immigrant students in New York City public schools. It provides credible evidence of these effects by exploiting the exogenous timing of natural disasters relative to testing dates in models with student fixed effects. Natural disasters in the home country lower immigrant students’ test scores in reading by 0.051 standard deviation, and by 0.028 standard deviation in mathematics. This paper provides strong evidence that the home country is an important out-of-school factor shaping immigrant students’ academic success and shows that children are affected by distal contexts in which they do not directly participate.
Hannah Arendt: Socratic Citizenship and Philosophical Critique
Authors: Villa Dana 
Published: July 2020

Abstract
In this essay I trace the relationship between philosophy and politics in Hannah Arendt’s work, with specific reference to the tension between her Socratic commitments and her appeal to “common sense” or sensus communis. I argue Arendt’s idea of a “common sense of the world” gives rise to a conception of the public realm that has too much shape and integrity to fit the often misty and particulate nature of contemporary reality. This is not the familiar critique of Arendt as a nostalgic Grecophile. Rather, it is a critique aimed at the phenomenological concept of “world” underlying her analysis. This concept—derived, but notably different, from Husserl’s and Heidegger’s respective conceptions—relies on background practices and understandings that are thick enough to sustain both a common public culture and a shared “sense of the world.” I suggest that Arendt’s appeal to a sensus communis runs aground of the moral and value pluralism that both Weber and Berlin have suggested are constitutive features of modernity. I conclude with some remarks on the relationship between Arendt’s critique of modernity and Socratic philosophical critique (on the one hand) and Frankfurt School Critical Theory (on the other).
The Pregnant Body and the Birth of the Other: Arendt’s Contribution to Original Ethics
Authors: Gaffney Jennifer 
Published: July 2020

Abstract
This paper examines Hannah Arendt’s contribution to recent debate concerning the urgency of Martin Heidegger’s original ethics. To this end, I turn to Arendt’s existential interpretation of birth as this takes shape in her discourse on the miracle. Though recent commentators have criticized Arendt’s emphasis on the miracle, I argue that she deepens a conversation about birth that Dennis Schmidt, following Jacques Derrida, has set in motion in his efforts to contribute to a more original ethics. Whereas Schmidt prioritizes the helplessness of the newborn, Arendt’s interpretation of the miracle suggests that birth reminds us not simply of our responsibility to help the helpless, but also of our responsibility to prepare the world for the incalculable possibilities of the newcomer. In this, I argue that Arendt brings into focus the ground of our responsibility to make space in the world for what cannot be reduced and decided on in advance by calculative procedure, thereby opening new paths to thinking the task of original ethics.
The predictive value of serum procalcitonin level as a prognostic marker for outcomes in out-of-hospital cardiac arrest patients
Authors: Shin Hyungoo , Lee Yoonje , Choi Hyuk Joong , Kim Changsun ,   for the Korean Cardiac Arrest Research Consortium (KoCARC) Investigators
Published: July 2020

Background: Patients who have successful return of spontaneous circulation after cardiac arrest may experience post-cardiac arrest syndrome. Procalcitonin can be used to assess the severity of post-cardiac arrest syndrome. The association between procalcitonin and outcomes in Asian patients with post-cardiac arrest syndrome has not been extensively studied. Objective: This study aimed to investigate the predictive value of serum procalcitonin level in the prognosis of patients hospitalized after out-of-hospital cardiac arrest. Methods: A retrospective observational study using the multicenter Korean Cardiac Arrest Research Consortium registry between October 2015 and June 2018 was performed. Serum procalcitonin level at the early phase of hospital presentation was obtained from the patients hospitalized after out-of-hospital cardiac arrest. In-hospital mortality and neurologic outcomes at hospital discharge were estimated. The relationship between serum procalcitonin level and in-hospital mortality and neurologic outcomes of patients was analyzed. Results: A total of 254 patients hospitalized after out-of-hospital cardiac arrest were included. Serum procalcitonin level was significantly elevated in non-survivors compared to survivors (0.17 (0.05–0.18) ng/dL vs. 0.10 (0.05–0.39) ng/dL, p = 0.017, respectively). In addition, serum procalcitonin level was significantly elevated in patients with unfavorable outcomes at hospital discharge compared to those with favorable outcomes (0.16 (0.06–1.10) ng/dL vs. 0.07 (0.04–0.22) ng/dL, p < 0.001, respectively). However, serum procalcitonin level had a weak predictive value for in-hospital mortality (area under the receiver operating characteristic curve: 0.587, 95% confidence interval: 0.517–0.657, p = 0.017, cut-off = 0.12 ng/dL, specificity = 57.4%) and unfavorable outcomes (area under the receiver operating characteristic curve: 0.646, 95% confidence interval: 0.571–0.721, p < 0.001, cut-off = 0.11 ng/dL, specificity = 62.3%). Conclusion: Elevated serum procalcitonin level in patients hospitalized after out-of-hospital cardiac arrest at the early phase of hospital presentation is associated with poor outcomes. However, serum procalcitonin level had weak diagnostic accuracy for predicting in-hospital mortality and unfavorable outcomes.
A Mendelian randomization of γ′ and total fibrinogen levels in relation to venous thromboembolism and ischemic stroke
Authors: Maners Jillian , Gill Dipender , Pankratz Nathan , Laffan Michael A. , Wolberg Alisa S. , de Maat Moniek P. M. , Ligthart Symen , Tang Weihong , Ward-Caviness Cavin K. , Fornage Myriam , Debette Stephanie , Dichgans Martin , McKnight Barbara , Boerwinkle Eric ,   CHARGE Inflammation Working Group,   INVENT Consortium,   MEGASTROKE consortium of the International Stroke Genetics Consortium (ISGC), Smith Nicholas L. , Morrison Alanna C. , Dehghan Abbas , de Vries Paul S. 
Published: July 2020

Abstract
Fibrinogen is a key component of the coagulation cascade, and variation in its circulating levels may contribute to thrombotic diseases, such as venous thromboembolism (VTE) and ischemic stroke. Gamma prime (γ′) fibrinogen is an isoform of fibrinogen that has anticoagulant properties. We applied 2-sample Mendelian randomization (MR) to estimate the causal effect of total circulating fibrinogen and its isoform, γ′ fibrinogen, on risk of VTE and ischemic stroke subtypes using summary statistics from genome-wide association studies. Genetic instruments for γ′ fibrinogen and total fibrinogen were selected, and the inverse-variance weighted MR approach was used to estimate causal effects in the main analysis, complemented by sensitivity analyses that are more robust to the inclusion of pleiotropic variants, including MR-Egger, weighted median MR, and weighted mode MR. The main inverse-variance weighted MR estimates based on a combination of 16 genetic instruments for γ′ fibrinogen and 75 genetic instruments for total fibrinogen indicated a protective effect of higher γ′ fibrinogen and higher total fibrinogen on VTE risk. There was also a protective effect of higher γ′ fibrinogen levels on cardioembolic and large artery stroke risk. Effect estimates were consistent across sensitivity analyses. Our results provide evidence to support effects of genetically determined γ′ fibrinogen on VTE and ischemic stroke risk. Further research is needed to explore mechanisms underlying these effects and their clinical applications.
Study on Cutting Force, Cutting Temperature and Machining Residual Stress in Precision Turning of Pure Iron with Different Grain Sizes
Authors: Yang Yinfei , Jin Lu , Zhu Jinpeng , Kong Jinxing , Li Liang 
Published: July 2020

AbstractPure iron is one of the difficult-to-machine materials due to its large chip deformation, adhesion, work-hardening, and built-up edges formation during machining. This leads to a large workpiece deformation and challenge to meet the required technical indicators. Therefore, under varying the grain size of pure iron, the influence of cutting speed, feed, and depth of cut on the cutting force, heat generation, and machining residual stresses were explored in the turning process to improve the machinability without compromising the mechanical properties of the material. The experimental findings have depicted that the influence of grain size on cutting force in the precision turning process is not apparent. However, the cutting temperature and residual stress of machining fine-grain iron were much smaller than the coarse grain at all levels of cutting parameters.
Co-dosing Ozone and Deionized Water as Oxidant Precursors of ZnO Thin Film Growth by Atomic Layer Deposition
Authors: Cheng Yung-Chen , Wang Hsiang-Chen , Feng Shih-Wei , Li Tsai-Pei , Fung Siu-Keung , Yuan Kai-Yun , Chen Miin-Jang 
Published: July 2020

AbstractCharacteristics of atomic layer deposition (ALD)-grown ZnO thin films on sapphire substrates with and without three-pulsed ozone (O3) as oxidant precursor and post-deposition thermal annealing (TA) are investigated. Deposition temperature and thickness of ZnO epilayers are 180 °C and 85 nm, respectively. Post-deposition thermal annealing is conducted at 300 °C in the ambience of oxygen (O2) for 1 h. With strong oxidizing agent O3 and post-deposition TA in growing ZnO, intrinsic strain and stress are reduced to 0.49% and 2.22 GPa, respectively, with extremely low background electron concentration (9.4 × 1015 cm−3). This is originated from a lower density of thermally activated defects in the analyses of thermal quenching of the integrated intensity of photoluminescence (PL) spectra. TA further facilitates recrystallization forming more defect-free grains and then reduces strain and stress state causing a remarkable decrease of electron concentration and melioration of surface roughness.
Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine
Authors: Khanal Piush , Maltecca Christian , Schwab Clint , Fix Justin , Bergamaschi Matteo , Tiezzi Francesco 
Published: July 2020

AbstractBackgroundThe objectives of this study were to evaluate genomic and microbial predictions of phenotypes for meat quality and carcass traits in swine, and to evaluate the contribution of host-microbiome interactions to the prediction. Data were collected from Duroc-sired three-way crossbred individuals (n = 1123) that were genotyped with a 60 k SNP chip. Phenotypic information and fecal 16S rRNA microbial sequences at three stages of growth (Wean, Mid-test, and Off-test) were available for all these individuals. We used fourfold cross-validation with animals grouped based on sire relatedness. Five models with three sets of predictors (full, informatively reduced, and randomly reduced) were evaluated. ‘Full’ included information from all genetic markers and all operational taxonomic units (OTU), while ‘informatively reduced’ and ‘randomly reduced’ represented a reduced number of markers and OTU based on significance preselection and random sampling, respectively. The baseline model included the fixed effects of dam line, sex and contemporary group and the random effect of pen. The other four models were constructed by including only genomic information, only microbiome information, both genomic and microbiome information, and microbiome and genomic information and their interaction.ResultsInclusion of microbiome information increased predictive ability of phenotype for most traits, in particular when microbiome information collected at a later growth stage was used. Inclusion of microbiome information resulted in higher accuracies and lower mean squared errors for fat-related traits (fat depth, belly weight, intramuscular fat and subjective marbling), objective color measures (Minolta a*, Minolta b* and Minolta L*) and carcass daily gain. Informative selection of markers increased predictive ability but decreasing the number of informatively reduced OTU did not improve model performance. The proportion of variation explained by the host-genome-by-microbiome interaction was highest for fat depth (~ 20% at Mid-test and Off-test) and shearing force (~ 20% consistently at Wean, Mid-test and Off-test), although the inclusion of the interaction term did not increase the accuracy of predictions significantly.ConclusionsThis study provides novel insight on the use of microbiome information for the phenotypic prediction of meat quality and carcass traits in swine. Inclusion of microbiome information in the model improved predictive ability of phenotypes for fat deposition and color traits whereas including a genome-by-microbiome term did not improve prediction accuracy significantly.
A topological data analysis based classification method for multiple measurements
Authors: Riihimäki Henri , Chachólski Wojciech , Theorell Jakob , Hillert Jan , Ramanujam Ryan 
Published: July 2020

Abstract
Background
Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network graph based on the data topology. A machine learning model with cross-validation is then applied for classification. When test this on three case studies, accuracy exceeds an alternative support vector machine (SVM) voting model in most situations tested, with additional benefits such as reporting data subsets with high purity along with feature values.

Results
For 100 examples of 3 different tree species, the model reached 80% classification accuracy after 30 datapoints, which was improved to 90% after increased sampling to 400 datapoints. The alternative SVM classifier achieved a maximum accuracy of 68.7%. Using data from 100 examples from each class of 6 different random point processes, the classifier achieved 96.8% accuracy, vastly outperforming the SVM. Using two outcomes in neuron spiking data, the TDA classifier was similarly accurate to the SVM in one case (both converged to 97.8% accuracy), but was outperformed in the other (relative accuracies 79.8% and 92.2%, respectively).

Conclusions
This algorithm and software can be beneficial for repeated measurement data common in biological sciences, as both an accurate classifier and a feature selection tool.
AdmixPipe: population analyses in Admixture for non-model organisms
Authors: Mussmann Steven M. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E. 
Published: July 2020

Abstract
Background
Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow these large datasets to be efficiently parsed are often lacking, or if indeed available, then limited by the necessity of a comparable reference genome as an adjunct. This, of course, can be difficult when working with non-model organisms. Fortunately, pipelines are currently available that avoid this prerequisite, thus allowing data to be a priori parsed. An oft-used molecular ecology program (i.e., Structure), for example, is facilitated by such pipelines, yet they are surprisingly absent for a second program that is similarly popular and computationally more efficient (i.e., Admixture). The two programs differ in that Admixture employs a maximum-likelihood framework whereas Structure uses a Bayesian approach, yet both produce similar results. Given these issues, there is an overriding (and recognized) need among researchers in molecular ecology for bioinformatic software that will not only condense output from replicated Admixture runs, but also infer from these data the optimal number of population clusters (K).

Results
Here we provide such a program (i.e., AdmixPipe) that (a) filters SNPs to allow the delineation of population structure in Admixture, then (b) parses the output for summarization and graphical representation via Clumpak. Our benchmarks effectively demonstrate how efficient the pipeline is for processing large, non-model datasets generated via double digest restriction-site associated DNA sequencing (ddRAD). Outputs not only parallel those from Structure, but also visualize the variation among individual Admixture runs, so as to facilitate selection of the most appropriate K-value.

Conclusions
AdmixPipe successfully integrates Admixture analysis with popular variant call format (VCF) filtering software to yield file types readily analyzed by Clumpak. Large population genomic datasets derived from non-model organisms are efficiently analyzed via the parallel-processing capabilities of Admixture. AdmixPipe is distributed under the GNU Public License and freely available for Mac OSX and Linux platforms at: https://github.com/stevemussmann/admixturePipeline.