bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Correlates and Outcomes of Dual Basiliximab and Antithymocyte Globulin Induction in Kidney Transplant Recipients: A National Study
Authors: Lam Ngan N. , Jeong Rachel , Quinn Robert R. , Ravani Pietro , Xiao Huiling , McAdams-DeMarco Mara , Axelrod David A. , Schnitzler Mark A. , Snyder Jon J. , Lentine Krista L. 
Published: July 2021

Background.
The unplanned use of dual induction therapy with interleukin-2 receptor-blocking antibodies (IL2rAb) and antithymocyte globulin (ATG) may portend adverse outcomes.

Methods.
We used national transplant registry data to study clinical correlates and outcomes of single versus dual induction therapy in adult kidney-only transplant recipients in the United States (2005–2018). The risk of death and graft loss at 1 and 5 y, according to induction therapy type, was assessed using multivariate Cox regression analysis (adjusted hazard ratio with 95% upper and lower confidence limits [LCLaHRUCL]).

Results.
Of the 157 351 recipients included in the study, 67% were treated with ATG alone, 29% were treated with IL2rAb alone, and 5% were treated with both. Compared with IL2rAb alone, the strongest correlates of dual induction included Black race, calculated panel reactive antibody ≥80%, prednisone-sparing maintenance immunosuppression, more recent transplant eras, longer cold ischemia time, and delayed graft function. Compared with ATG alone, dual induction was associated with an increased 5-y risk of death (aHR 1.071.151.23; P < 0.0001), death-censored graft failure (aHR 1.051.131.22; P < 0.05), and all-cause graft failure (aHR 1.061.121.18; P < 0.0001).

Conclusions.
Further research is needed to develop risk-prediction tools to further inform optimal, individualized induction protocols for kidney transplant recipients.
Variation in Evolving Optic Neuritis
Authors: Bouffard Marc A. , Mallery Robert M. , Liao Yaping J. , Torun Nurhan 
Published: July 2021

Background:
The typical natural history of optic neuritis is subjected to important exceptions. Recognition of these exceptions has led to valuable insights regarding specific etiologies of optic neuritis. Exceptions to the natural history of recovering optic neuritis are well-defined (e.g., chronic relapsing inflammatory optic neuropathy), but exceptions to the natural history of evolving optic neuritis are less so.

Methods:
Medical records of patients illustrating an atypical course of evolving optic neuritis were reviewed in a retrospective manner. Each patient was treated by at least one of the authors.

Results:
Four patients were identified who illustrated an atypical natural history of incipient optic neuritis. Diagnoses included idiopathic optic neuritis, seropositive neuromyelitis optica spectrum disease, anti-myelin oligodendrocyte glycoprotein antibody disease, and multiple sclerosis in 1 patient each. Features of interest included an atypical temporal relationship between development of pain and onset of clinical optic neuropathy, an unusually protracted duration of pain, and an unusually long duration of worsening optic neuropathy before stabilization.

Conclusions:
This case series illustrates the substantial clinical heterogeneity which may be observed in the evolution of optic neuritis. The temporal relationship between development of pain and onset of clinical optic neuropathy, the duration of pain, and duration of worsening optic neuropathy before stabilization are all subjected to significant variability. Although most patients with optic neuritis present with painful vision loss which progresses over 1 week or less, careful attention to the exceptions described herein may facilitate earlier recognition of diagnostically challenging cases.
Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan
Authors: Sawada Hiroyuki , Fujikawa Takashi , Satou Mamoru 
Published: July 2021

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus

Pseudomonas

and are closely related to

Pseudomonas cedrina

subsp.

cedrina

CFML 96-198T (99.72 %),

Pseudomonas cedrina

subsp.

fulgida

P515/12T (99.65 %),

Pseudomonas gessardii

DSM 17152T (99.51 %),

Pseudomonas synxantha

DSM 18928T (99.44 %),

Pseudomonas libanensis

CIP 105460T (99.44 %) and

Pseudomonas lactis

DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1
ω7c/C16 : 1
ω6c), C16 : 0 and summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the

Pseudomonas fluorescens

subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel

Pseudomonas

species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).
Altered functional connectome hierarchy with gene expression signatures in newly-diagnosed focal epilepsy
Authors: de Bézenac Christophe E , Caciagli Lorenzo , Alonazi Batil K , Bernhardt Boris C , Marson Anthony G , Keller Simon S 
Published: July 2021

AbstractObjectiveNeuroimaging research is providing insights into epilepsy as a disorder of brain connectivity linked to functional impairments which may have an identifiable genetic component. This case-control study aims to identify imbalances in a functional connectome dimension spanning from unimodal to transmodal networks and explore the potential genetic basis of such alterations in patients with newly diagnosed focal epilepsy (NDfE).MethodsWe used gradient-based analysis of resting-sate fMRI data comparing cortical gradient maps in patients with NDfE (n = 27) to age and sex-matched controls (n = 36). Using a brain-wide gene expression dataset, gene combinations associated with altered brain regions were then entered into an enrichment analysis.ResultsWe found an increased differentiation of connectivity profiles between unimodal and transmodal networks in NDfE, which was particularly pronounced in the patients with persistent seizures at 12-months follow-up (n=10). Differences corresponded to gradient score reductions in a visual network and increases in limbic and default mode systems which subserve higher-level cognition. Cortical difference maps were spatially correlated with regional expression of a weighted gene combination. These genes were enriched for disease and ontology terms and pathways previously associated with epilepsy and seizure susceptibility.InterpretationsLarge-scale functional hierarchy may be altered from in focal epilepsy from diagnosis and correlate with response to treatment. Combining functional neuroimaging and transcriptional data analysis may provide a framework for understanding the wide-ranging impairments associated with the disorder and mechanistic insight into how gene processes may drive alterations in brain function mediating the genetic risk of epilepsy.
The devil is in the details: Reporting and transparent research practices in sports medicine and orthopedic clinical trials
Authors: Schulz Robert , Langen Georg , Prill Robert , Cassel Michael , Weissgerber Tracey 
Published: July 2021

AbstractIntroductionWhile transparent reporting of clinical trials is essential to assess the risk of bias and translate research findings into clinical practice, earlier studies have shown that deficiencies are common. This study examined current clinical trial reporting and transparent research practices in sports medicine and orthopedics.MethodsThe sample included clinical trials published in the top 25% of sports medicine and orthopedics journals over nine months. Two independent reviewers assessed pre-registration, open data and criteria related to scientific rigor, the study sample, and data analysis.ResultsThe sample included 163 clinical trials from 27 journals. While the majority of trials mentioned rigor criteria, essential details were often missing. Sixty percent (confidence interval [CI] 53-68%) of trials reported sample size calculations, but only 32% (CI 25-39%) justified the expected effect size. Few trials indicated the blinding status of all main stakeholders (4%; CI 1-7%). Only 18% (CI 12-24%) included information on randomization type, method, and concealed allocation. Most trials reported participants’ sex/gender (95%; CI 92-98%) and information on inclusion and exclusion criteria (78%; CI 72-84%). Only 20% (CI 14-26%) of trials were pre-registered. No trials deposited data in open repositories.ConclusionsThese results will aid the sports medicine and orthopedics community in developing tailored interventions to improve reporting. While authors typically mention blinding, randomization and other factors, essential details are often missing. Greater acceptance of open science practices, like pre-registration and open data, is needed. These practices have been widely encouraged, we discuss systemic interventions that may improve clinical trial reporting.Registrationhttps://doi.org/10.17605/OSF.IO/9648H
Recruitment of highly functional SARS-CoV-2-specific CD8+T cell receptors mediating cytotoxicity of virus-infected target cells in non-severe COVID-19
Authors: Wagner Karolin I. , Mateyka Laura M. , Jarosch Sebastian , Grass Vincent , Weber Simone , Schober Kilian , Hammel Monika , Burrell Teresa , Kalali Behnam , Poppert Holger , Beyer Henriette , Schambeck Sophia , Holdenrieder Stefan , Strötges-Achatz Andrea , Haselmann Verena , Neumaier Michael , Erber Johanna , Priller Alina , Yazici Sarah , Roggendorf Hedwig , Odendahl Marcus , Tonn Torsten , Dick Andrea , Witter Klaus , Mijočević Hrvoje , Protzer Ulrike , Knolle Percy A. , Pichlmair Andreas , Crowell Claudia S. , Gerhard Markus , D’Ippolito Elvira , Busch Dirk H. 
Published: July 2021

ABSTRACTT cell immunity is crucial for the control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and has been widely characterized on a quantitative level. In contrast, the quality of such T cell responses has been poorly investigated, in particular in the case of CD8+T cells. Here, we explored the quality of SARS-CoV-2-specific CD8+T cell responses in individuals who recovered from mild symptomatic infections, through which protective immunity should develop, by functional characterization of their T cell receptor (TCR) repertoire. CD8+T cell responses specific for SARS-CoV-2-derived epitopes were low in frequency but could be detected robustly early as well as late - up to twelve months - after infection. A pool of immunodominant epitopes, which accurately identified previous SARS-CoV-2 infections, was used to isolate TCRs specific for epitopes restricted by common HLA class I molecules. TCR-engineered T cells showed heterogeneous functional avidity and cytotoxicity towards virus-infected target cells. High TCR functionality correlated with gene signatures of T cell function and activation that, remarkably, could be retrieved for each epitope:HLA combination and patient analyzed. Overall, our data demonstrate that highly functional HLA class I TCRs are recruited and maintained upon mild SARS-CoV-2 infection. Such validated epitopes and TCRs could become valuable tools for the development of diagnostic tests determining the quality of SARS-CoV-2-specific CD8+T cell immunity, and thereby investigating correlates of protection, as well as to restore functional immunity through therapeutic transfer of TCR-engineered T cells.
Positive and negative stroke signs revisited: dissociations between synergies, weakness, and impaired reaching dexterity
Authors: Hadjiosif Alkis. M. , Branscheidt Meret , Anaya Manuel A. , Runnalls Keith D. , Keller Jennifer , Bastian Amy J. , Celnik Pablo A. , Krakauer John W. 
Published: July 2021

AbstractMost stroke victims experience motor deficits, usually referred to collectively as hemiparesis. While hemiparesis is one of the most common and clinically recognizable motor abnormalities, it remains under-characterized in terms of its behavioral subcomponents and their interactions. Hemiparesis is comprised of both negative and positive motor signs. Negative signs consist of weakness and loss of motor control (dexterity), whereas positive signs consist of spasticity, abnormal resting posture, and intrusive movement synergies (abnormal muscle co-activations during voluntary movement). How positive and negative signs interact, and whether a common mechanism generates them, remains poorly understood. Here we employed a planar, arm-supported reaching task to assess post-stroke arm dexterity loss, which we compared to the Fugl-Meyer stroke scale; a measure primarily reflecting abnormal synergies. We examined 53 patients with hemiparesis after a first-time ischemic stroke. Reaching kinematics were markedly more impaired in patients with subacute (<3 months) compared to chronic (>6 months) stroke even when matched for Fugl-Meyer score. This suggests a dissociation between abnormal synergies (reflected in the Fugl-Meyer scale) and loss of dexterity, which in turn suggests different underlying mechanisms. Moreover, dynamometry suggested that Fugl-Meyer scores capture weakness as well as abnormal synergies, in line with these two deficits sharing a neural substrate. These findings have two important implications: First, clinical studies that test for efficacy of rehabilitation interventions should specify which component of hemiparesis they are targeting and how they propose to measure it. Second, there may be an opportunity to design rehabilitation interventions to address specific subcomponents of hemiparesis.
Reduced neutralizing activity of post-SARS-CoV-2 vaccination serum against variants B.1.617.2, B.1.351, B.1.1.7+E484K and a sub-variant of C.37
Authors: Carreño Juan Manuel , Alshammary Hala , Singh Gagandeep , Raskin Ariel , Amanat Fatima , Amoako Angela , Gonzalez-Reiche Ana Silvia , van de Guchte Adriana ,   PARIS study group, Awawda Mahmoud , Banu Radhika , Beach Katherine , Bermúdez-González Carolina , Bielak Dominika , Cao Liyong , Chernet Rachel , Desai Parnavi , Fabre Shelcie , Ferreri Emily. D. , Floda Daniel , Gleason Charles , Kawabata Hisaaki , Khan Zenab , Kleiner Giulio , Jurczyszak Denise , Matthews Julia , Mendez Wanni , Mulder Lubbertus CF , Paniz-Mondolfi Kayla Dr. Alberto E , Russo  , Salimbangon Ashley , Saksena Miti , Shin A. , Sominsky Levy , Tcheou Johnston , Srivastava Komal , Sordillo Emilia Mia , Sather D. Noah , van Bakel Harm , Krammer Florian , Simon Viviana 
Published: July 2021

AbstractHighly efficacious vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed.1 However, the emergence of viral variants that are more infectious than the earlier SARS-CoV-2 strains is concerning.2 Several of these viral variants have the potential to partially escape neutralizing antibody responses warranting continued immune-monitoring. Here, we tested a number of currently circulating viral variants of concern/interest, including B.1.526 (Iota), B.1.1.7+E484K (Alpha), B.1.351 (Beta), B.1.617.2 (Delta) and C.37 (Lambda) in neutralization assays using a panel of post-mRNA vaccination sera. The assays were performed with authentic SARS-CoV-2 clinical isolates in an assay that mimics physiological conditions. We found only small decreases in neutralization against B.1.526 and an intermediate phenotype for B.617.2. The reduction was stronger against a sub-variant of C.37, followed by B.1.351 and B.1.1.7+E484K. C.37 is currently circulating in parts of Latin America3 and was detected in Germany, the US and Israel. Of note, reduction in a binding assay that also included P.1, B.1.617.1 (Kappa) and A.23.1 was negligible. Taken together, these findings suggest that mRNA SARS-CoV-2 vaccines may remain effective against these viral variants of concern/interest and that spike binding antibody tests likely retain specificity in the face of evolving SARS-CoV-2 diversity.
RTT109 and Fun30 proteins mediate epigenetic regulation of the DNA damage response pathway in C. albicans
Authors: Garai Pramita , Maurya Prashant Kumar , Bhatt Himanshu , Goyal Aarti , Dewasthale Sakshi , Gupta Meghna , Haokip Dominic Thangminlen , Muthuswami Rohini 
Published: July 2021

ABSTRACTFun30, an ATP-dependent chromatin remodeller, from S. cerevisiae mediates both regulation of gene expression as well as DNA damage response/repair. In this paper, we have characterized the biochemical and physiological function of Fun30 from the opportunistic fungi, C. albicans. Biochemically, the protein shows DNA-stimulated ATPase activity. Physiologically, the protein co-regulates transcription of RTT109, TEL1, MEC1, and SNF2-genes that encode for proteins involved in DNA damage response and repair pathway. The expression of FUN30, in turn, is regulated by histone H3 acetylation catalysed by Rtt109 encoded by RTT109. The RTT109Hz/FUN30Hz mutant strain shows sensitivity to oxidative stress and resistance to MMS as compared to the wild type strain. Quantitative PCR showed that the sensitivity to oxidative stress results from downregulation of MEC1, RAD9, MRC1 and RAD5 expression; ChIP experiments showed Fun30 but not H3ac regulates the expression of these genes in response to oxidative stress. In contrast, on treatment with MMS, the expression of RAD9 is upregulated and this upregulation is co-regulated by both Fun30 and H3 acetylation catalysed by Rtt109. Thus, Fun30 and H3 acetylation mediate the response of the fungal cell to genotoxic agents in C. albicans by regulating the expression of DNA damage response and repair pathway genes.
The framework of plant regeneration in duckweed (Lemna turonifera) comprises genetic transcript regulation and cyclohexane release
Authors: Yang Lin , Sun Jinge , Yao Jie , Wang Yaya , Yan Congyu , Wu Junyi , Ren Qiuting , Zhao Ling , Sun Jinsheng 
Published: July 2021

AbstractRegeneration is important for vegetative propagation of excellent variety, detoxification and the obtain of transgenic plant, but plant regeneration is time-consuming. Here, we found that duckweed regeneration could be enhanced by regenerating callus. Firstly, Genetic transcript regulation has been applied to study the molecular mechanism controlling regeneration. Auxin related genes have been significantly down-regulated in regenerating callus. Cytokinin signal pathway genes have been up-regulated in regenerating callus. Secondly, volatile organic compounds release has been analysised by gas chromatography/mass spectrum during the stage of plant regeneration, and 11 kinds of unique volatile organic compounds in the regenerating callus were increased. Among them, cyclohexane treatment enhanced duckweed regeneration by initiating root. Moreover, Auxin signal pathway genes were down-regulated in callus treated by cyclohexane. All together, these results provide novel mechanistic insights into how regenerating callus promotes duckweed regeneration.Graphical abstract
Reducing indoor particle exposure using mobile air purifiers - experimental and numerical analysis
Authors: Tobisch Adrian , Springsklee Lukas , Schäfer Lisa-Franziska , Sussmann Nico , Lehmann Martin J. , Weis Frederik , Zöllner Raoul , Niessner Jennifer 
Published: July 2021

AbstractAerosol particles are one of the main routes of transmission of COVID-19. Mobile air purifiers are used to reduce the risk of infection indoors. We focus on an air purifier which generates a defined volumetric air flow through a highly efficient filter material. We investigate the transport of aerosol particles from an infected dummy equipped with an aerosol generator to receiving thermal dummies. For analysis, we use up to 12 optical particle counters to monitor the particle concentration with high spatial resolution. Based on the measurement data, a computational fluid dynamics (CFD) model is set up and validated. The experimental and numerical methods are used to investigate how the risk of infection suggested by the particle exposure in an exemplary lecture hall can be reduced by a clever choice of orientation of the air purifier. The particle concentration at head height deviates by 13 % for variations of location and orientation. Finally, CFD simulation was used to monitor the particle fates. The steady simulation results fit quite well to the experimental findings and provide additional information about particle path and for assessing comfort level due to air flow.Practical implicationsDifferent installation locations and operating conditions of the air purifier are evaluated and the use of thermal dummies mimics the conditions of practical use cases. The measurement results show the integral particle mass over time in the “faces of the dummies”, representing the potentially inhaled particle load of persons present in the room. At an air change per hour of 5, the cumulated PM1 mass at head level was reduced by 75 %, independently of the location of the infected dummy, compared to the “natural decay” case showing that filtration is an effective means of reducing aerosol particle concentrations. It turns out that obstructing the outlet stream of the air purifier may be particularly advantageous.
A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks
Authors: Kato Masaki , Iwakoshi-Ukena Eiko , Furumitsu Megumi , Ukena Kazuyoshi 
Published: July 2021

ABSTRACTWe recently discovered a novel cDNA encoding the precursor of a small secretory protein, neurosecretory protein GM (NPGM), in the mediobasal hypothalamus of chickens. Although our previous study showed that subcutaneous infusion of NPGM for 6 days increased body mass in chicks, the chronic effect of intracerebroventricular (i.c.v.) infusion of NPGM remains unknown. In this study, chronic i.c.v. infusion of NPGM for 2 weeks significantly increased body mass, water intake, and the mass of abdominal fat in chicks, whereas NPGM did not affect food intake, muscle mass, or blood glucose concentration. Morphological analyses revealed that fat accumulation occurred in both liver and abdominal fat. These results indicate that NPGM may participate in fat storage in chicks.