bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variants in CLDN5 cause a syndrome characterized by seizures, microcephaly and brain calcifications
Authors: Deshwar Ashish R , Cytrynbaum Cheryl , Murthy Harsha , Zon Jessica , Chitayat David , Volpatti Jonathan , Newbury-Ecob Ruth , Ellard Sian , Allen Hana Lango , Yu Emily P , Noche Ramil , Walker Suzi , Scherer Stephen W , Mahida Sonal , Elitt Christopher M , Nicolas Gaël , Goldenberg Alice , Saugier-Veber Pascale , Lecoquierre Francois , Dabaj Ivana , Meddaugh Hannah , Marble Michael , Keppler-Noreuil Kim M , Drayson Lucy , Barañano Kristin W , Chassevent Anna , Agre Katie , Létard Pascaline , Bilan Frederic , Le Guyader Gwenaël , Laquerrière Annie , Ramsey Keri , Henderson Lindsay , Brady Lauren , Tarnopolsky Mark , Bainbridge Matthew , Friedman Jennifer , Capri Yline , Athayde Larissa , Kok Fernando , Gurgel-Giannetti Juliana , Ramos Luiza L P , Blaser Susan , Dowling James J , Weksberg Rosanna 
Published: December 2022

Abstract
The blood–brain barrier ensures CNS homeostasis and protection from injury. Claudin-5 (CLDN5), an important component of tight junctions, is critical for the integrity of the blood–brain barrier. We have identified de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. All variants clustered in one subregion/domain of the CLDN5 gene and the recurrent variants demonstrate genotype–phenotype correlations. We modelled both patient variants and loss of function alleles in the zebrafish to show that the variants analogous to those in patients probably result in a novel aberrant function in CLDN5. In total, human patient and zebrafish data provide parallel evidence that pathogenic sequence variants in CLDN5 cause a novel neurodevelopmental disorder involving disruption of the blood–brain barrier and impaired neuronal function.
HTNV infection induces activation and deficiency of CD8+MAIT cells in HFRS patients
Authors: Zhang Yusi , Wang Meng , Zhang Xiyue , Tang Kang , Zhang Chunmei , Jia Xiaozhou , Hu Haifeng , Liu He , Li Na , Zhuang Ran , Jin Boquan , Ma Ying , Zhang Yun 
Published: December 2022

Abstract
Hantaan virus (HTNV) infection causes an epidemic of hemorrhagic fever with renal syndrome (HFRS) mainly in Asia. Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes known to play an important role in innate host defense during virus infection. However, their roles and phenotypes during HTNV infection have not yet been explored. We characterized CD8+MAIT cells from HFRS patients based on scRNA-seq data combined with flow cytometry data. We showed that HTNV infection caused the loss and activation of CD8+MAIT cells in the peripheral blood, which were correlated with disease severity. The production of granzyme B and IFN-γ from CD8+MAIT cells and the limitation of HTNV replication in endothelia cells indicated the anti-viral property of CD8+MAIT cells. In addition, in vitro infection of MAIT cells by HTNV or HTNV-exposed monocytes showed that the activation of MAIT cells was IL-18 mediated. In conclusion, this study identified, for the first time, gene expression profiles of MAIT cells, provided underlying molecular mechanisms for activation of MAIT cells during HTNV infection, and suggested a potential anti-viral role of MAIT cells in HFRS.
Specific clinical vignettes in high-risk protected percutaneous coronary intervention
Authors: Panoulas Vasileios , Tan Sian-Tsung , Hill Jonathan , Tarantini Giuseppe 
Published: December 2022

AbstractThere are several cardiac- and patient-related factors that come into play when considering patients for protected percutaneous coronary intervention (PCI). Cardiac factors include complexity/location of coronary lesions, the degree of left or right ventricular impairment, the presence of valvular lesions, and ventricular arrhythmias. Patient related factors include comorbidities that would render the patient at a higher risk of death should cardiogenic shock ensue during the procedure. Comorbidities include chronic lung disease (chronic obstructive airways disease, asthma, pulmonary fibrosis), renal or liver impairment, other cardiovascular diseases (such as previous cerebrovascular accident or transient ischemic attack, peripheral arterial disease, carotid stenosis), diabetes, frailty and advanced age. Here, we present three very different cases where left ventricular support was deemed appropriate to reduce peri-procedural risk and optimize outcomes.
Chitosan-modified fluorescent dye for simple, fast, and in-situ measurement of fungal cell growth in the presence of insoluble compounds
Authors: Yang Zihuayuan , Hu Xin , Zhang Funing , Durrani Samran , Zhang Jie , Pang Ai-Ping , Gao Yichen , Wu Fu-Gen , Lin Fengming 
Published: December 2022

Abstract
The measurement of fungal cell growth in submerged culture systems containing insoluble compounds is essential yet difficult due to the interferences from the insoluble compounds like biopolymers. Here, we developed a fluorescent strategy based on chitosan-modified fluorescein isothiocyanate (GC-FITC) to monitor the cell growth of lignocellulosic fungi cultivated on biopolymers. GC-FITC could stain only lignocellulosic fungi (Tricoderma reesei, Penicillium oxalicum, Aspergillus nidulans, and Neurospora crassa), but not biopolymers (cellulose, xylan, pectin, or lignin), excluding the interferences from these insoluble biopolymer. Moreover, a linear relationship was observed between the fluorescence intensity of GC-FITC absorbed by lignocellulosic fungi and the biomass of lignocellulosic fungi. Therefore, GC-FITC was leveraged to monitor the cell growth of lignocellulosic fungi when using biopolymers like cellulose as the carbon sources, which is faster, more convenient, time-saving, and cost-effective than the existing methods using protein/DNA content measurement. GC-FITC offers a powerful tool to detect fungal growth in culture systems with insoluble materials.
Determination of the viscoelastic parameters for the generalized viscoelastic wave equation
Authors: Xu Qiang , Wang Yanghua 
Published: December 2022

SUMMARY
The viscoelasticity of subsurface media is succinctly represented in the generalized wave equation by a fractional time derivative. This generalized viscoelastic wave equation is characterized by the viscoelastic parameter and the viscoelastic velocity, but these parameters are not well formulated and therefore unfavourable for seismic implementation. Here, we prove that the generalized wave equation is causal and stable by deriving the rate-of-relaxation function. Causality and stability are two necessary conditions for the applicability of the wave equation in seismic simulations. On this basis, we determine the physical parameters for the application of the generalized wave equation. First, we formulate the relationship between the viscoelastic parameter and the constant Q model. The proposed frequency-independent relation agrees with the theoretical solution and fits the field data. Then, we formulate the viscoelastic velocity in terms of the reference velocity and the viscoelastic parameter. These two formulations adequately represent the viscoelastic effect in seismic wave propagation and lead to an improvement in the accuracy of the numerical simulation of the generalized viscoelastic wave equation.
Association of liver dysfunction with outcomes after cardiac surgery—a meta-analysis
Authors: Kirov Hristo , Caldonazo Tulio , Audisio Katia , Rahouma Mohamed , Robinson N Bryce , Cancelli Gianmarco , Soletti Giovanni J , Demetres Michelle , Ibrahim Mudathir , Faerber Gloria , Gaudino Mario , Doenst Torsten 
Published: December 2022

Abstract

OBJECTIVES
The aim of this study was to perform a meta-analysis of studies reporting outcomes in patients with liver dysfunction addressed by the model of end-stage liver disease and Child–Turcotte–Pugh scores undergoing cardiac surgery.

METHODS
A systematic literature search was conducted to identify contemporary studies reporting short- and long-term outcomes in patients with liver dysfunction compared to patients with no or mild liver dysfunction undergoing cardiac surgery (stratified in high and low score group based on the study cut-offs). Primary outcome was perioperative mortality. Secondary outcomes were perioperative neurological events, prolonged ventilation, sepsis, bleeding and/or need for transfusion, acute kidney injury and long-term mortality.

RESULTS
A total of 33 studies with 48 891 patients were included. Compared with the low score group, being in the high score group was associated with significantly higher risk of perioperative mortality [odds ratio (OR) 3.72, 95% confidence interval (CI) 2.75–5.03, P &lt; 0.001]. High score group was also associated with a significantly higher rate of perioperative neurological events (OR 1.49, 95% CI 1.30–1.71, P &lt; 0.001), prolonged ventilation (OR 2.45, 95% CI 1.94–3.09, P &lt; 0.001), sepsis (OR 3.88, 95% CI 2.07–7.26, P &lt; 0.001), bleeding and/or need for transfusion (OR 1.95, 95% CI 1.43–2.64, P &lt; 0.001), acute kidney injury (OR 3.84, 95% CI 2.12–6.98, P &lt; 0.001) and long-term mortality (incidence risk ratio 1.29, 95% CI 1.14–1.46, P &lt; 0.001)

CONCLUSIONS
The analysis suggests that liver dysfunction in patients undergoing cardiac surgery is independently associated with higher risk of short and long-term mortality and also with an increased occurrence of various perioperative adverse events.
Reassessment of the Broth Microdilution Method for Susceptibility Testing of Helicobacter pylori
Authors: Tang Xiaoqiong , Shen Yalin , Song Xiaona , Benghezal Mohammed , Marshall Barry J , Tang Hong , Li Hong 
Published: December 2022

Abstract

Background
Helicobacter pylori infection is an infectious disease and thus the eradication treatment should be guided by susceptibility testing. This study aimed to assess the applicability of broth microdilution as a routine susceptibility testing method for H. pylori.

Methods
Susceptibility profiles of clarithromycin (CLR) and levofloxacin (LEV) resistance in 76 clinical H. pylori isolates were simultaneously assessed using agar dilution and broth microdilution methods. The correlation between the minimum inhibitory concentrations (MICs) obtained by the 2 methods was assessed by means of linear regression analysis.

Results
The correlation between the MICs determined by broth microdilution method and agar dilution method was good for both CLR (r = 0.966) and LEV (r = 0.959). The susceptibility agreement between the 2 methods was 100% for CLR and 96.1% for LEV. Using the broth microdilution method, the false resistance was found in 3.9% (3 of 76) strains for LEV susceptibility testing. No false susceptibility was found for either CLR or LEV, and no false resistance was found for susceptibility testing of CLR.

Conclusions
The broth microdilution method is suitable for routine susceptibility testing of clinical H. pylori isolates.
The Inappropriateness of Using Rifampicin E-Test to Predict Rifabutin Resistance in Helicobacter pylori
Authors: Yang Tiankuo , Liu Bowen , Zhou Junpeng , Shen Yalin , Song Xiaona , Tang Xiaoqiong , Benghezal Mohammed , Marshall Barry James , Tang Hong , Li Hong 
Published: December 2022

Abstract

Background
The aim of this study was to evaluate the rifamycin cross-resistance in Helicobacter pylori, and whether the use of rifampicin E-test strips to screen H. pylori rifabutin resistance is appropriate.

Methods
A total of 89 H. pylori isolates were included. Rifampicin minimum inhibitory concentrations (MICs) were obtained by E-test, while the MICs for rifapentine, rifaximin, and rifabutin were determined by agar dilution method. The rifamycin resistance rates based on different breakpoints were compared. Isolates with high-level rifampicin resistance were subjected to whole-genome sequencing.

Results
A wide distribution of MICs (mostly in the range 0.125–8 mg/L) was observed for rifampicin, rifapentine, and rifaximin. Using MIC &gt;1, ≥ 4, and &gt; 4 mg/L as the breakpoints, resistance rates to rifampicin/rifapentine/rifaximin were 60.4%/48.3%/38.2%, 28.1%/25.8%/23.6%, and 15.7%/16.9%/7.9%, respectively. However, the rifabutin MICs of all the tested H. pylori isolates were extremely low (≤0.016 mg/L). Applying MIC ≥ 0.125 mg/L as the breakpoint, rifabutin resistance was nil. No mutation was found in the rpoB gene sequences of the 2 isolates with high-level rifampicin resistance.

Conclusions
There is a lack of cross-resistance between rifabutin and other rifamycins in H. pylori. The use of rifampicin E-test to predict H. pylori rifabutin resistance is inappropriate.
Exploring the in situ evolution of nitrofurantoin resistance in clinically derived uropathogenic Escherichia coli isolates
Authors: Vallée Maxime , Harding Chris , Hall Judith , Aldridge Phillip D , TAN Aaron 
Published: December 2022

Abstract

Background
Nitrofurantoin has been re-introduced as a first-choice antibiotic to treat uncomplicated acute urinary tract infections in England and Wales. Highly effective against common uropathogens such as Escherichia coli, its use is accompanied by a low incidence (&lt;10%) of antimicrobial resistance. Resistance to nitrofurantoin is predominantly via the acquisition of loss-of-function, step-wise mutations in the nitroreductase genes nfsA and nfsB.

Objective
To explore the in situ evolution of NitR in E. coli isolates from 17 patients participating in AnTIC, a 12-month open label randomized controlled trial assessing the efficacy of antibiotic prophylaxis in reducing urinary tract infections (UTIs) incidence in clean intermittent self-catheterizing patients.

Methods
The investigation of NitR evolution in E. coli used general microbiology techniques and genetics to model known NitR mutations in NitSE. coli strains.

Results
Growth rate analysis identified a 2%–10% slower doubling time for nitrofurantoin resistant strains: NitS: 20.8 ± 0.7 min compared to NitR: 23 ± 0.8 min. Statistically, these data indicated no fitness advantage of evolved strains compared to the sensitive predecessor (P-value = 0.13). Genetic manipulation of E. coli to mimic NitR evolution, supported no fitness advantage (P-value = 0.22). In contrast, data argued that a first-step mutant gained a selective advantage, at sub-MIC (4–8 mg/L) nitrofurantoin concentrations.

Conclusion
Correlation of these findings to nitrofurantoin pharmacokinetic data suggests that the low incidence of E. coli NitR, within the community, is driven by urine-based nitrofurantoin concentrations that selectively inhibit the growth of E. coli strains carrying the key first-step loss-of-function mutation.
Characterizing the macrostructure of electronic health record work using raw audit logs: an unsupervised action embeddings approach
Authors: Lou Sunny S , Liu Hanyang , Harford Derek , Lu Chenyang , Kannampallil Thomas 
Published: December 2022

AbstractRaw audit logs provide a comprehensive record of clinicians’ activities on an electronic health record (EHR) and have considerable potential for studying clinician behaviors. However, research using raw audit logs is limited because they lack context for clinical tasks, leading to difficulties in interpretation. We describe a novel unsupervised approach using the comparison and visualization of EHR action embeddings to learn context and structure from raw audit log activities. Using a dataset of 15 767 634 raw audit log actions performed by 88 intern physicians over 6 months of EHR use across inpatient and outpatient settings, we demonstrated that embeddings can be used to learn the situated context for EHR-based work activities, identify discrete clinical workflows, and discern activities typically performed across diverse contexts. Our approach represents an important methodological advance in raw audit log research, facilitating the future development of metrics and predictive models to measure clinician behaviors at the macroscale.
Maize Inbred Mp708 is Highly Susceptible to Western Corn Rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), in Field and Greenhouse Assays
Authors: Pereira Adriano E , Geisert Ryan W , Hibbard Bruce E 
Published: December 2022

Abstract
The western corn rootworm (WCR), Diabrotica vifgirera virgifera LeConte, (Coleoptera: Chrysomelidae) causes significant economic damage in corn production each year. Resistance to insecticides and transgenic corn with Bacillus thuringiensis (Bt), Berliner toxins have been reported throughout the United States Corn Belt. Corn breeding programs for natural resistance against WCR larvae could potentially assist in rootworm management. Root damage and root regrowth of eight corn lines were evaluated in field assays at three different locations. Results indicated the inbred ‘Mp708’ had the greatest root damage and was significantly greater than damage for the susceptible control, B37×H84. In greenhouse assays, we evaluated four of these lines plus a hybrid expressing the mCry3A Bt toxin for damage. The results indicated that Mp708 had significantly higher root damage when compared to ‘CRW3(S1)C6’ and ‘MIR604’. Despite previous work suggesting otherwise, we conclude that Mp708 is highly susceptible to the WCR larvae based on root damage in field and greenhouse plant assays.
Community-level predictions in a megadiverse hotspot: comparison of stacked species distribution models to forest inventory data
Authors: Zwiener Victor Pereira , Alves Valéria Andressa 
Published: December 2022

AbstractGiven the current scenario of climate change and anthropogenic impacts, spatial predictions of biodiversity are fundamental to support conservation and restoration actions. Here, we compared different stacked species distribution models (S-SDMs) to forest inventories to assess if S-SDMs capture emerging properties and geographic patterns of species richness and composition of local communities in a biodiversity hotspot. We generated SDMs for 1499 tree species sampled in 151 sites across the Atlantic Forest. We applied four model stacking approaches to reconstruct the plant communities: binary SDMs (bS-SDMs), binary SDMs cropped by minimum convex polygons (bS-SDMs-CROP), stacked SDMs constrained by the observed species richness (cS-SDMs) and minimum convex polygons of species occurrences (MCPs). We compared the stacking methods with local communities in terms of species richness, composition, community prediction metrics and components of beta diversity—nestedness and turnover. S-SDMs captured general patterns, with bS-SDMs-CROP being the most parsimonious approach. Species composition differed between local communities and all stacking methods, in which bS-SDMs, bS-SDMs-CROP and MCPs followed a nested pattern, whereas species turnover was most important in cS-SDMs. S-SDMs varied in terms of performance, omission and commission errors, leading to a misprediction of some vulnerable, endangered and critically endangered species. Despite differing from forest inventory data, S-SDMs captured part of the variation from local communities, representing the potential species pool. Our results support the use of S-SDMs to endorse biodiversity synthesis and conservation planning at coarse scales and warn of potential misprediction at local scales in megadiverse regions.
SAMI-H i: The H i view of the Hα Tully–Fisher relation and data release
Authors: Catinella Barbara , Cortese Luca , Tiley Alfred L , Janowiecki Steven , Watts Adam B , Bryant Julia J , Croom Scott M , d’Eugenio Francesco , van de Sande Jesse , Bland-Hawthorn Joss , Fraser-McKelvie Amelia , Richards Samuel N , Sweet Sarah M , Pisano Daniel J , Pingel Nickolas , Koopmann Rebecca A , Cottrill Dillion , Hill Meghan 
Published: December 2022

ABSTRACT
We present SAMI-H i, a survey of the atomic hydrogen content of 296 galaxies with integral field spectroscopy available from the SAMI Galaxy Survey. The sample spans nearly 4 dex in stellar mass ($M_\star = 10^{7.4}-10^{11.1}~ \rm M_\odot$), redshift z &lt; 0.06, and includes new Arecibo observations of 153 galaxies, for which we release catalogues and H i spectra. We use these data to compare the rotational velocities obtained from optical and radio observations and to show how systematic differences affect the slope and scatter of the stellar-mass and baryonic Tully–Fisher relations. Specifically, we show that $\rm H\alpha$ rotational velocities measured in the inner parts of galaxies (1.3 effective radii in this work) systematically underestimate H i global measurements, with H i/$\rm H\alpha$ velocity ratios that increase at low stellar masses, where rotation curves are typically still rising and $\rm H\alpha$ measurements do not reach their plateau. As a result, the $\rm H\alpha$ stellar mass Tully–Fisher relation is steeper (when M⋆ is the independent variable) and has larger scatter than its H i counterpart. Interestingly, we confirm the presence of a small fraction of low-mass outliers of the $\rm H\alpha$ relation that are not present when H i velocity widths are used and are not explained by ‘aperture effects’. These appear to be highly disturbed systems for which $\rm H\alpha$ widths do not provide a reliable estimate of the rotational velocity. Our analysis reaffirms the importance of taking into account differences in velocity definitions as well as tracers used when interpreting offsets from the Tully–Fisher relation, at both low and high redshifts and when comparing with simulations.
Mapping variations of redshift distributions with probability integral transforms
Authors: Myles J , Gruen D , Amon A , Alarcon A , DeRose J , Everett S , Dodelson S , Bernstein G M , Campos A , Harrison I , MacCrann N , McCullough J , Raveri M , Sánchez C , Troxel M A , Yin B , Abbott T M C , Allam S , Alves O , Andrade-Oliveira F , Bertin E , Brooks D , Burke D L , Rosell A Carnero , Kind M Carrasco , Carretero J , Cawthon R , Costanzi M , da Costa L N , Pereira M E S , Desai S , Doel P , Ferrero I , Flaugher B , Frieman J , García-Bellido J , Gatti M , Gerdes D W , Gruendl R A , Gschwend J , Gutierrez G , Hartley W G , Hinton S R , Hollowood D L , Honscheid K , James D J , Kuehn K , Lahav O , Melchior P , Mena-Fernández J , Menanteau F , Miquel R , Mohr J J , Palmese A , Paz-Chinchón F , Pieres A , Malagón A A Plazas , Prat J , Rodriguez-Monroy M , Sanchez E , Scarpine V , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , Tucker D L , Vincenzi M , Weaverdyck N ,   (DES Collaboration)
Published: December 2022

ABSTRACT
We present a method for mapping variations between probability distribution functions and apply this method within the context of measuring galaxy redshift distributions from imaging survey data. This method, which we name PITPZ for the probability integral transformations it relies on, uses a difference in curves between distribution functions in an ensemble as a transformation to apply to another distribution function, thus transferring the variation in the ensemble to the latter distribution function. This procedure is broadly applicable to the problem of uncertainty propagation. In the context of redshift distributions, for example, the uncertainty contribution due to certain effects can be studied effectively only in simulations, thus necessitating a transfer of variation measured in simulations to the redshift distributions measured from data. We illustrate the use of PITPZ by using the method to propagate photometric calibration uncertainty to redshift distributions of the Dark Energy Survey Year 3 weak lensing source galaxies. For this test case, we find that PITPZ yields a lensing amplitude uncertainty estimate due to photometric calibration error within 1 per cent of the truth, compared to as much as a 30 per cent underestimate when using traditional methods.