bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Operando calorimeter for high temperature electrochemical cells
Authors: Young David , Jackson Ariel , Fork David , Sadat Seid , Rettenwander Daniel , Benck Jesse D , Chiang Yet-Ming 
Published: September 2020

Abstract

Operando calorimetry has previously been utilized to study electrochemical reactions and degradation in electrochemical cells such as batteries. Calorimetric data can provide important information on the lifetime and thermal properties of electrochemical cells in practical engineering applications such as thermal management. High temperature electrochemical cells such as solid oxide fuel cells or electrolyzers can also benefit from operando calorimetry, but to the authors’ knowledge such capabilities have not been commercially developed. Herein, an operando calorimeter is reported that is capable of simultaneous calorimetry and electrochemistry at temperatures up to 1000 °C and in both oxidizing and reducing atmospheres. The calorimeter is constructed by modifying a commercial apparatus originally designed to study high temperature electrochemical cells in various gas environments. A grey-box, nonlinear system identification model is utilized to analyze both electrochemical and calorimetric data of BaZr0.8Ce0.1Y0.1O3 based electrochemical cells and achieve a calorimeter electrochemical cell power sensitivity of 16.1 ± 11.7 mW. This operando calorimeter provides the capability to study thermal behaviour of electrochemical cells at elevated temperatures.
Impact of Fat Graft Thickness and Harvesting Technique on Adipocyte Viability in a New Porcine Experimental Model: An Immunohistochemical Analysis
Authors: de Arruda Eduardo Gustavo Pires , Munhoz Alexandre Mendonça , Matsumoto Walter , Ueda Thiago , Montag Eduardo , Okada Alberto , Coudry Renata de Almeida , de Castro Isac , Gemperli Rolf 
Published: September 2020

Abstract

Background
Autologous fat grafting (AFG) has been employed in surgical practice as a filling method. However, controversies remain on the specifics of this technique. So far, few relevant experimental large animal studies have objectively assessed factors related to AFG integration.

Objectives
This study utilized an experimental, medium-sized animal model to compare the feasibility of AFG collected employing 2 different techniques with instruments of distinct thicknesses.

Methods
Twenty minipigs (Sus scropha domesticus) were subjected to AFG harvesting via en bloc resection utilizing 3- (Group I) and 5-mm-diameter (Group II) round punch blades (PBs) and liposuction (LS) with 3- (Group III) and 5-mm-diameter cannulas (Group IV). Both samples were grafted intramuscularly (biceps femoralis). Hematoxylin and eosin staining was employed to identify intact adipocytes, fat necrosis, fibrosis, inflammation, and oil cysts. Immunohistochemical staining (perilipin-A, tumor necrosis factor alfa, and cluster of differentiation number 31) was utilized to quantify the feasibility of adipocytes, tissue necrosis, and neoangiogenesis, respectively.

Results
Hematoxylin and eosin analysis showed that fat necrosis and histiocyte presence were significantly lower in the AFG harvested utilizing a PB than in LS. For perilipin-A, a statistical difference was observed between subgroups I and III (P = 0.001) and I and IV (P = 0.004). Instrument diameter had no effect on graft integration in comparisons between groups II and III (P = 0.059) and II and IV (P = 0.132).

Conclusions
In this experimental study, fat collected utilizing a PB demonstrated higher adipocyte viability than fat collected with LS. The diameter of the collection instruments, whether PB or LS, had no effect on graft integration.
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery
Authors: Shao Hongzhao , Boulton Stephen , Olivieri Cristina , Mohamed Hebatallah , Akimoto Madoka , Subrahmanian Manu Veliparambil , Veglia Gianluigi , Markley John L , Melacini Giuseppe , Lee Woonghee 
Published: September 2020

Abstract

Motivation
Correlated Nuclear Magnetic Resonance (NMR) chemical shift changes identified through the CHEmical Shift Projection Analysis (CHESPA) and CHEmical Shift Covariance Analysis (CHESCA) reveal pathways of allosteric transitions in biological macromolecules. To address the need for an automated platform that implements CHESPA and CHESCA and integrates them with other NMR analysis software packages, we introduce here integrated plugins for NMRFAM-SPARKY that implement the seamless detection and visualization of allosteric networks.

Availability and implementation
CHESCA-SPARKY and CHESPA-SPARKY are available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers to the SBGrid (https://sbgrid.org). The assigned spectra involved in this study and tutorial videos using this dataset are available at https://sites.google.com/view/chescachespa-sparky.

Supplementary information
Supplementary data are available at Bioinformatics Online.
Annotating high-impact 5′untranslated region variants with the UTRannotator
Authors: Zhang Xiaolei , Wakeling Matthew , Ware James , Whiffin Nicola 
Published: September 2020

Abstract

Summary
Current tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. Variants outside of these regions may have a large impact on protein expression and/or structure and can lead to disease, but this effect can be challenging to predict. Consequently, these variants are poorly annotated using standard tools. We have developed a plugin to the Ensembl Variant Effect Predictor, the UTRannotator, that annotates variants in 5′untranslated regions (5′UTR) that create or disrupt upstream open reading frames. We investigate the utility of this tool using the ClinVar database, providing an annotation for 31.9% of all 5′UTR (likely) pathogenic variants, and highlighting 31 variants of uncertain significance as candidates for further follow-up. We will continue to update the UTRannotator as we gain new knowledge on the impact of variants in UTRs.

Availability and implementation
UTRannotator is freely available on Github: https://github.com/ImperialCardioGenetics/UTRannotator.

Supplementary information
Supplementary data are available at Bioinformatics online.
Increased Callosal Connectivity in Reeler Mice Revealed by Brain-Wide Input Mapping of VIP Neurons in Barrel Cortex
Authors: Hafner Georg , Guy Julien , Witte Mirko , Truschow Pavel , Rüppel Alina , Sirmpilatze Nikoloz , Dadarwal Rakshit , Boretius Susann , Staiger Jochen F 
Published: September 2020

AbstractThe neocortex is composed of layers. Whether layers constitute an essential framework for the formation of functional circuits is not well understood. We investigated the brain-wide input connectivity of vasoactive intestinal polypeptide (VIP) expressing neurons in the reeler mouse. This mutant is characterized by a migration deficit of cortical neurons so that no layers are formed. Still, neurons retain their properties and reeler mice show little cognitive impairment. We focused on VIP neurons because they are known to receive strong long-range inputs and have a typical laminar bias toward upper layers. In reeler, these neurons are more dispersed across the cortex. We mapped the brain-wide inputs of VIP neurons in barrel cortex of wild-type and reeler mice with rabies virus tracing. Innervation by subcortical inputs was not altered in reeler, in contrast to the cortical circuitry. Numbers of long-range ipsilateral cortical inputs were reduced in reeler, while contralateral inputs were strongly increased. Reeler mice had more callosal projection neurons. Hence, the corpus callosum was larger in reeler as shown by structural imaging. We argue that, in the absence of cortical layers, circuits with subcortical structures are maintained but cortical neurons establish a different network that largely preserves cognitive functions.
Host cell death during infection withChlamydia: a double-edged sword
Authors: Sixt Barbara S 
Published: September 2020

ABSTRACTThe phylum Chlamydiae constitutes a group of obligate intracellular bacteria that infect a remarkably diverse range of host species. Some representatives are significant pathogens of clinical or veterinary importance. For instance, Chlamydia trachomatis is the leading infectious cause of blindness and the most common bacterial agent of sexually transmitted diseases. Chlamydiae are exceptionally dependent on their eukaryotic host cells as a consequence of their developmental biology. At the same time, host cell death is an integral part of the chlamydial infection cycle. It is therefore not surprising that the bacteria have evolved exquisite and versatile strategies to modulate host cell survival and death programs to their advantage. The recent introduction of tools for genetic modification of Chlamydia spp., in combination with our increasing awareness of the complexity of regulated cell death in eukaryotic cells, and in particular of its connections to cell-intrinsic immunity, has revived the interest in this virulence trait. However, recent advances also challenged long-standing assumptions and highlighted major knowledge gaps. This review summarizes current knowledge in the field and discusses possible directions for future research, which could lead us to a deeper understanding of Chlamydia’s virulence strategies and may even inspire novel therapeutic approaches.
How to feel French: the politics of community and emotion in the siege of Paris (1649)
Authors: Coons James 
Published: September 2020

Abstract
As royal forces besieged Parisian frondeur rebels in early 1649, pamphleteers developed potent rhetorical tools to rally virtuous French people against the foreign enemies in their midst. Authors mixed contemporary conceptions of emotion with accepted wisdom on embodied traits in order to bind their audience together. Their vision of patrie community was defined by love and sacrifice for the innocent French, and rage against the foreigners who persecuted them. The rout of frondeur forces at the battle of Charenton on 8 February 1649 provided a tragic, but useful opportunity to distil this message. Propagandists imagined encounters between the royalist general Condé and his slain friend and lieutenant Châtillon to clarify the emotions and actions befitting a true Frenchman, in the throes of a burgeoning civil war. Even in the face of a stinging defeat, rebel authors effectively made shared emotions the foundation of a ‘pure’ French community.
The morality of “ get-threats”: Withholding divorce as extortion
Authors: Rivlin Ram 
Published: September 2020

Abstract
Threatening to withhold Jewish divorce in order to extract concessions, which I term here the “get-threat,” is widely regarded as extortionist. Yet this view is commonly associated with skepticism towards agreements stemming from unequal bargaining power, or with a progressive view of the proper divorce regime. Building on contemporary discussions of what is known as “the paradox of blackmail” this article argues that in many cases get-threats should be regarded as simple cases of extortion even by libertarians and conservatives. It then presents and analyzes the best possible statement of defense for the practice of get-threats, designed for the “reasonable reactionary,” showing that even from that point of view get-threats should be limited in scope and magnitude to a narrow range of cases of justified, reasonable demands. The article thus offers both a precise analysis of a longstanding debate and a normative argument for its proper resolution.
Challenges and Promise of Human Immunodeficiency Virus Remission
Authors: Li Yijia , Mohammadi Abbas , Li Jonathan Z 
Published: September 2020

Abstract
Antiretroviral therapy effectively controls human immunodeficiency virus (HIV) replication but it is unable to fully eradicate the HIV reservoir and treatment must be life-long. Progress toward a strategy for HIV remission will require overcoming key hurdles to fill gaps in our understanding of HIV persistence, but the identification of individuals who have attained sterilizing or functional HIV cure show that such a goal is achievable. In this review, we first outline challenges in targeting the HIV reservoir, including difficulties identifying HIV-infected cells, ongoing work elucidating the complex intracellular environment that contribute to HIV latency, and barriers to reactivating and clearing the HIV reservoir. We then review reported cases of HIV sterilizing cure and explore natural models of HIV remission and the promise that such HIV spontaneous and posttreatment controllers may hold in our search for a broadly-applicable strategy for the millions of patients living with HIV.
Multi-phenotypic and bi-directional behavioral screening of zebrafish larvae
Authors: Khalili Arezoo , van Wijngaarden Ellen , Zoidl Georg R , Rezai Pouya 
Published: September 2020

Abstract
Multi-phenotypic screening of zebrafish larvae, such as monitoring the heart and tail activities, is important in biological assays. Microfluidic devices have been developed for zebrafish phenotypic assays, but simultaneous lateral–dorsal screening of the same larva in a single chip is yet to be achieved. We present a multi-phenotypic microfluidic device for monitoring of tail movement and heart rate (HR) of 5–7-day postfertilization zebrafish larvae. Tail movements were stimulated using electric current and quantified in terms of response duration (RD) and tail beat frequency (TBF). The positioning of a right-angle prism provided a lateral view of the larvae and enabled HR monitoring. Investigations were performed on zebrafish larvae exposed to 3% ethanol, 250 μM 6-hydroxydopamine (6-OHDA) or 1 mM levodopa. Larvae exposed to ethanol showed a significant drop in HR, whereas electric stimulation increased the HR temporarily. Larvae experienced a significant drop in RD, TBF and HR when exposed to 6-OHDA. HR was not affected by levodopa post-treatment, whereas RD and TBF were restored to normal levels. The results showed potential for applications that involve monitoring of cardiac and behavioral parameters in zebrafish larvae. Tests can be done using the same chip, without changing the larvae’s orientation. This eliminates undue stress caused by reorientation, which may affect their behavior, and the use of separate devices to obtain dorsal and lateral views. The device can be implemented to improve multi-phenotypic and quantitative screening of zebrafish larvae in response to chemical and physical stimuli in different zebrafish disease models.
Activity of β-lactam/taniborbactam (VNRX-5133) combinations against carbapenem-resistant Gram-negative bacteria
Authors: Mushtaq Shazad , Vickers Anna , Doumith Michel , Ellington Matthew J , Woodford Neil , Livermore David M 
Published: September 2020

AbstractBackgroundBoronates are of growing interest as β-lactamase inhibitors. The only marketed analogue, vaborbactam, principally targets KPC carbapenemases, but taniborbactam (VNRX-5133, Venatorx) has a broader spectrum.MethodsMICs of cefepime and meropenem were determined combined with taniborbactam or avibactam for carbapenem-resistant UK isolates. β-Lactamase genes and porin alterations were sought by PCR or sequencing.ResultsTaniborbactam potentiated partner β-lactams against: (i) Enterobacterales with KPC, other class A, OXA-48-like, VIM and NDM (not IMP) carbapenemases; and (ii) Enterobacterales inferred to have combinations of ESBL or AmpC activity and impermeability. Potentiation of cefepime (the partner for clinical development) by taniborbactam was slightly weaker than by avibactam for Enterobacterales with KPC or OXA-48-like carbapenemases, but MICs of cefepime/taniborbactam were similar to those of ceftazidime/avibactam, and the spectrum was wider. MICs of cefepime/taniborbactam nonetheless remained &gt;8 + 4 mg/L for 22%–32% of NDM-producing Enterobacterales. Correlates of raised cefepime/taniborbactam MICs among these NDM Enterobacterales were a cefepime MIC &gt;128 mg/L, particular STs and, for Escherichia coli only: (i) the particular blaNDM variant (even though published data suggest all variants are inhibited similarly); (ii) inserts in PBP3; and (iii) raised aztreonam/avibactam MICs. Little or no potentiation of cefepime or meropenem was seen for Pseudomonas aeruginosa and Acinetobacter baumannii with MBLs, probably reflecting slower uptake or stronger efflux. Potentiation of cefepime was seen for Stenotrophomonas maltophilia and Elizabethkingia meningoseptica, which have both chromosomal ESBLs and MBLs.ConclusionsTaniborbactam broadly reversed cefepime or meropenem non-susceptibility in Enterobacterales and, less reliably, in non-fermenters.
Public attitudes toward an authorization for contact program for clinical research
Authors: Niyibizi Nyiramugisha K , Speight Candace D , Gregor Charlie , Ko Yi-An , Kraft Stephanie A , Mitchell Andrea R , Phillips Bradley G , Porter Kathryn M , Shah Seema K , Sugarman Jeremy , Wilfond Benjamin S , Dickert Neal W 
Published: September 2020

AbstractWe conducted an online experimental survey to evaluate attitudes toward an authorization for contact (AFC) program allowing researchers to contact patients about studies based on electronic record review. A total of 1070 participants were randomly assigned to 1 of 3 flyers varying in design and framing. Participants were asked to select concerns about and reasons for signing up for AFC. Logistic regression and latent class analysis were conducted. The most commonly selected concerns included needing more information (43%), privacy (40%), and needing more time to think (28%). A minority were not interested in participating in research (16%) and did not want to be bothered (15%). Latent class analysis identified clusters with specific concerns about privacy, lack of interest in research, and not wanting to be bothered. A novel flyer with simple and positive framing was associated with lower odds of both not wanting to be bothered (P = .01) and not being interested in research (P = .01). Many concerns about AFC programs appear nonspecific. Addressing privacy, lack of interest in research, and not wanting to be bothered warrant further study as ways to enhance recruitment.
Development of an Assay to Determine the Amount of Ca-Fatty Acid Soaps in Feces
Authors: Stroebinger Natascha , Rutherfurd Shane M , Henare Sharon J , Moughan Paul J 
Published: September 2020

AbstractBackgroundThe quantification of fecal Ca-fatty acid soaps is important to understand how fatty acids behave in the gastrointestinal tract.ObjectiveAs current methods to extract Ca-fatty acid soaps from feces give low recoveries an accurate assay to determine the amount of fatty acid soaps in feces was developed.MethodCa-fatty acid soaps are determined indirectly after non-soap fatty acid compounds have been extracted from the feces. Synthetic Ca-fatty acid soaps of different chain lengths (C12–C18) and degree of saturation (C18:0–C18:2) were incubated with several solvents to find the solvents that least-solubilize the Ca-fatty acid soaps. A three-step extraction was devised using extractions with hexane, hexane-isopropanol and water either at room temperature or at 60°C, 37°C, or 80°C, respectively. Feces were spiked with free fatty acids, Ca-fatty acid soaps, Na-fatty acid salts, and phospholipids.ResultsAll of the free fatty acids and phospholipids and almost all of the Na-fatty acid salts were removed and 98% of Ca-lauric acid soap, 99% of Ca-stearic acid soap, and 93% of oleic acid soap were recovered.ConclusionsThe method is suitable for determining fatty acids in the form of Ca-fatty acid soaps in feces.HighlightsNew method to determine fecal Ca-fatty acid soaps. Consistent and high recovery of fatty acid-soaps.
Impact of previous thoracic radiation therapy on the efficacy of immune checkpoint inhibitors in advanced non small cell lung cancer
Authors: Hosokawa Shinobu , Ichihara Eiki , Bessho Akihiro , Harada Daijiro , Inoue Koji , Shibayama Takuo , Kishino Daizo , Harita Shingo , Ochi Nobuaki , Oda Naohiro , Hara Naofumi , Hotta Katsuyuki , Maeda Yoshinobu , Kiura Katsuyuki 
Published: September 2020

Abstract

Objectives
Studies investigating the association between radiation therapy and the efficacy of immune checkpoint inhibitors in advanced non-small-cell lung cancer have provided inconsistent results, likely due to relatively small cohort sizes. This study investigated the effect of previous thoracic radiation therapy on the efficacy of immune checkpoint inhibitor therapy in a large non-small-cell lung cancer cohort.

Patients and methods
We conducted a retrospective cohort study using data from 531 non-small-cell lung cancer patients who received monotherapy with programmed cell death protein 1/programmed death-ligand 1 inhibitors at nine institutions. The effects of thoracic radiation therapy on the efficacy of immune checkpoint inhibitors were investigated.

Results
A total of 531 non-small-cell lung cancer patients treated with immune checkpoint inhibitors were included in this study. The progression-free survival period was significantly longer in patients that had received thoracic radiation therapy before immune checkpoint inhibitor therapy compared to those without previous thoracic radiation therapy (median progression-free survival 5.0 vs. 3.0 months, P = 0.0013). A multivariate analysis showed that thoracic radiation therapy was an independent predictive factor of improved progression-free survival (hazard ratio of progression-free survival: 0.79, P = 0.049). In contrast, extra-thoracic radiation therapy was associated with inferior outcomes (median progression-free survival 3.0 vs. 4.2 months, P = 0.0008).

Conclusion
Previous thoracic radiation therapy, but not prior extra-thoracic radiation therapy, enhanced the efficacy of anti-programmed cell death protein 1/programmed death-ligand 1 therapy in non-small-cell lung cancer patients.
Constraining nucleosynthesis in two CEMP progenitors using fluorine
Authors: Mura-Guzmán Aldo , Yong D , Abate C , Karakas A , Kobayashi C , Oh H , Chun S-H , Mace G 
Published: September 2020

ABSTRACT
We present new fluorine abundance estimations in two carbon enhanced metal-poor (CEMP) stars, HE 1429−0551 and HE 1305+0007. HE 1429−0551 is also enriched in slow neutron-capture process (s-process) elements, a CEMP-s, and HE 1305+0007 is enhanced in both, slow and rapid neutron-capture process elements, a CEMP-s/r. The F abundances estimates are derived from the vibration–rotation transition of the HF molecule at 23358.6 Å using high-resolution infrared spectra obtained with the Immersion Grating Infrared Spectrometer (IGRINS) at the 4-m class Lowell Discovery Telescope. Our results include an F abundance measurement in HE 1429−0551 of A(F) = +3.93 ([F/Fe] = +1.90) at [Fe/H] = −2.53, and an F upper limit in HE 1305+0007 of A(F) &lt; +3.28 ([F/Fe] &lt; +1.00) at [Fe/H] = −2.28. Our new derived F abundance in HE 1429−0551 makes this object the most metal-poor star where F has been detected. We carefully compare these results with literature values and state-of-the-art CEMP-s model predictions including detailed asymptotic giant branch (AGB) nucleosynthesis and binary evolution. The modelled fluorine abundance for HE 1429−0551 is within reasonable agreement with our observed abundance, although is slightly higher than our observed value. For HE 1429−0551, our findings support the scenario via mass transfer by a primary companion during its thermally pulsing phase. Our estimated upper limit in HE 1305+0007, along with data from the literature, shows large discrepancies compared with AGB models. The discrepancy is principally due to the simultaneous s- and r-process element enhancements which the model struggles to reproduce.