bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atrial Metastasis From Sarcomatoid Renal Cell Carcinoma
Authors: Filippi Luca , Iannarelli Angelo , Ambrogi Cesare , Bagni Oreste 
Published: September 2020

Abstract
We describe the case of a 54-year-old woman, previously submitted to nephrectomy for sarcomatoid renal cell carcinoma and treated with antibiotics because of central venous catheter infection. An 18F-FDG PET/CT scan was obtained that demonstrated bone and lymph node metastases and also disclosed an irregular area of highly increased uptake (SUVmax 19.4) in the right atrium. Clinical data did not suggest a relapsed infection. A contrast-enhanced CT examination of the heart enabled the diagnosis of intra-atrial metastasis. Furthermore, integration between PET and cardiac 3-dimensional volume rendering proved useful for defining the anatomical relationships between atrial metastasis and large vessels.
Visceral Metastases as Predictors of Response and Survival Outcomes in Patients of Castration-Resistant Prostate Cancer Treated With 177Lu-Labeled Prostate-Specific Membrane Antigen Radioligand Therapy
Authors: Satapathy Swayamjeet , Mittal Bhagwant Rai , Sood Ashwani 
Published: September 2020

Background
The presence of visceral metastases is associated with poor prognosis in patients of metastatic castration-resistant prostate cancer (mCRPC) treated with hormonal therapy and chemotherapy. However, studies evaluating its impact on treatment outcomes with 177Lu-labeled prostate-specific membrane antigen (PSMA) radioligand therapy (RLT) are currently limited and show inconsistent results. This systematic review was conducted to precisely evaluate the impact of visceral metastases on biochemical response and survival outcomes in patients of mCRPC treated with 177Lu-PSMA RLT.

Methods
This systematic review followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. Searches in PubMed, Scopus, and EMBASE were made using relevant keywords, and articles up to May 2020 were included. Univariate and multivariate odds ratios and hazard ratios (HRs) were extracted from the individual articles, and pooled estimates were generated using meta-analysis.

Results
Twelve articles comprising 1504 patients were included in this review. Presence of visceral metastases not only predicted low biochemical response rate (pooled univariate odds ratio: 0.38, 95% confidence interval [CI], 0.22–0.66) but was also a significant prognosticator of worse progression-free survival (pooled univariate HR, 1.85; 95% CI, 1.39–2.46; and pooled multivariate HR, 1.48; 95% CI, 1.15–1.92) and overall survival (pooled univariate HR, 1.77; 95% CI, 1.29–2.44; and pooled multivariate HR, 2.22; 95% CI, 1.82–2.70). There was no evidence of publication bias.

Conclusions
Presence of visceral metastases was associated with poor response and survival outcomes in patients of mCRPC treated with 177Lu-PSMA RLT. The results are clinically significant for pretreatment risk stratification of such patients and to guide optimal treatment strategies.
Golf-Related Craniofacial Injuries in Adults: A NEISS Database Study
Authors: Brennan Matthew J. , Fish Sarah , Cohn Jason E. , Othman Sammy , Stucker Fred J. , Bundrick Paige 
Published: September 2020

Introduction:
Despite its popularity, there have been no reports outlining adult craniofacial trauma in the setting of golf injuries. Our main objective was to identify and describe trends in head and neck injuries incurred while participating in golf including injury type, anatomic location, and patient disposition.

Methods:
A retrospective cohort analysis of the National Electronic Injury Surveillance System (NEISS) was conducted from 2009–2018. Population characteristics of golf-related injuries were recorded, including, age, sex, and race distributions. Distribution of injury anatomic location, injury type, distribution of fracture location, patient disposition was further analyzed. A one way ANOVA was utilized to obtain the mean ages for all injuries and compare them for any statistical difference. To identify statistical significance, a Fisher exact test with a Monte Carlo simulation was performed.

Results:
A total of 509 golf-related injuries (national estimate 24,425 cases) were recorded over the study period. Lacerations were the most common injury overall (54.2%), while contusions and abrasions were the next most common injuries (27.3%). The most common fracture subtype observed was midface (40.43%), followed by nasal bone (27.66%), mandible (12.77%), skull (12.77%), and cervical spine (6.38%). The highest proportion of patients admitted for further treatment were individuals >70 years of age. Fractures had the highest rate of admission (29.8%).

Conclusions:
A better understanding of golf injuries can allow for rapid detection and appropriate treatment when encountered. This knowledge can also help to develop safety precautions by potentially reforming rules and regulations as well as protective equipment.
Needs Assessment for Lower Urinary Tract Injury Curriculum for FPMRS Fellowships
Authors: Mueller Margaret G. , Corton Marlene , Kenton Kimberly 
Published: September 2020

Objective
The aim of this study was to determine the level and types of training Accreditation Council for Graduate Medical Education–accredited programs use for female pelvic medicine and reconstructive surgery (FPMRS) fellows’ education on lower urinary tract injuries (LUTIs).

Methods
Two surveys were developed to assess the need for LUTI curriculum from both program director (PD) and fellow vantages through a multistage process, including review by knowledgeable colleagues, cognitive interviews, and pilot testing. Surveys were distributed in an electronic link via e-mail to graduating fellows and program directors from each of the 58 Accreditation Council for Graduate Medical Education–accredited FPMRS programs.

Results
Thirty-four graduating FPMRS fellows (71%) and 39 FPMRS PDs (67%) completed the survey. Both PDs and fellows responded that both the evaluation and management of LUTI were necessary to FPMRS training. The majority of PDs use a combination of didactics and hands-on learning in the operating room (60% and 71%). Only 40% and 30% incorporate simulation into the curriculum to address LUTI. Graduating fellows report low numbers of procedures to evaluate and manage LUTI. Specifically, only 15% of fellows graduate with greater than 2 ureteral reimplantations and 44% graduate with no minimally invasive abdominal vesicovaginal fistula repairs. The majority of graduating fellows reported feeling prepared to evaluate for LUTI, but nearly one third do not feel ready to independently manage LUTI upon graduation.

Conclusions
FPMRS PDs and fellows agree that the evaluation and management of LUTI are important; however, most programs use only didactics and hands-on learning in the operating room with extremely low case volumes, leading to decreased proficiency.
Predictive Modelling of COVID-19 New Cases in Algeria using An Extreme Learning Machines (ELM)
Authors: Djeddou Messaoud , Hameed Ibrahim A. , Nejatian Abolfazl , Loukam Imed 
Published: September 2020

AbstractIn this research, an extreme learning machine (ELM) is proposed to predict the new COVID-19 cases in Algeria. In the present study, public health database from Algeria health ministry has been used to train and test the ELM models.The input parameters for the predictive models include Cumulative Confirmed COVID-19 Cases (CCCC), Calculated COVID-19 New Cases (CCNC), and Index Day (ID).The predictive accuracy of the seven models has been assessed via several statistical parameters. The results showed that the proposed ELM model achieved an adequate level of prediction accuracy with smallest errors (MSE= 0.16, RMSE=0.4114, and MAE= 0.2912), and highest performance’s (NSE = 0.9999, IO = 0.9988, R2 = 0.9999). Hence, the ELM model could be utilized as a reliable and accurate modeling approach for predicting the new COVIS-19 cases in Algeria.The proposed ELM model, it can be used as a decision support tool to manage public health medical efforts and facilities against the COVID-19 pandemic crisis.
Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein
Authors: Paul Debamita , Mu Hong , Tavakoli Amirrasoul , Dai Qing , Chen Xuejing , Chakraborty Sagnik , He Chuan , Ansari Anjum , Broyde Suse , Min Jung-Hyun 
Published: September 2020

ABSTRACTXPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively ‘opening’ these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a ‘kinetic gating’ mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how ‘opening’ is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed ‘open’ undamaged DNA in solution and that such ‘opening’ can largely occur without one or the other of the β-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound ‘open’ DNA adopts multiple conformations in solution notwithstanding the DNA’s original structure or the β-hairpins. Molecular dynamics simulations reveal compensatory roles of the β-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA ‘opening’ of undamaged sites and the dynamic nature of ‘open’ DNA may shed light on how the protein functions within and beyond NER in cells.
Probabilistic mapping of human functional brain networks identifies regions of high group consensus
Authors: Dworetsky Ally , Seitzman Benjamin A. , Adeyemo Babatunde , Neta Maital , Coalson Rebecca S. , Petersen Steven E. , Gratton Caterina 
Published: September 2020

AbstractMany recent developments surrounding the functional network organization of the human brain have focused on data that have been averaged across groups of individuals. While such group-level approaches have shed considerable light on the brain’s large-scale distributed systems, they conceal individual differences in network organization, which recent work has demonstrated to be common and widespread. This individual variability produces noise in group analyses, which may average together regions that are part of different functional systems across participants, limiting interpretability. However, cost and feasibility constraints may limit the possibility for individual-level mapping within studies. Here our goal was to leverage information about individual-level brain organization to probabilistically map common functional systems and identify locations of high inter-subject consensus for use in future group analyses. We probabilistically mapped 14 functional networks in multiple datasets with relatively high amounts of data. All networks show “core” (high-probability) regions, but differ from one another in the extent of their higher-variability components. These patterns replicate well across four datasets with different participants and scanning parameters. We produced a set of high-probability regions of interest (ROIs) from these probabilistic maps; these and the probabilistic maps are made publicly available, together with a tool for querying the network membership probabilities associated with any given cortical location. These quantitative estimates and public tools may allow researchers to apply information about inter-subject consensus to their own fMRI studies, improving inferences about systems and their functional specializations.
A framework for mutational signature analysis based on DNA shape parameters
Authors: Karolak Aleksandra , Levatić Jurica , Supek Fran 
Published: September 2020

AbstractThe mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathematical construct obtained by a deconvolution of mutation frequency spectra across individuals. There is a need to enhance methods for inferring mutational signatures to make better use of sparse mutation data (e.g., resulting from exome sequencing of cancers), to facilitate insight into underlying biological mechanisms, and to provide more accurate mutation rate baselines for inferring positive and negative selection. We propose a conceptualization of mutational signatures that represents oligonucleotidesviadescriptors of DNA conformation: base pair, base pair step, and minor groove width parameters. We demonstrate how such DNA structural parameters can accurately predict mutation occurrence due to DNA repair failures or due to exposure to diverse mutagens such as radiation, chemical exposure, and the APOBEC cytosine deaminase enzymes. Furthermore, the mutation frequency of DNA oligomers classed by structural features can accurately capture systematic variability in mutagenesis of >1,000 tumors originating from diverse human tissues. A nonnegative matrix factorization was applied to mutation spectra stratified by DNA structural features, thereby extracting novel mutational signatures. Moreover, many of the known trinucleotide signatures were associated with an additional spectrum in the DNA structural descriptor space, which may aid interpretation and provide mechanistic insight. Overall, we suggest that the power of DNA sequence motif-based mutational signature analysis can be enhanced by drawing on DNA shape features.
Impaired online error-correction disrupts synchronization to external events in autism
Authors: Vishne Gal , Jacoby Nori , Malinovitch Tamar , Epstein Tamir , Frenkel Or , Ahissar Merav 
Published: September 2020

AbstractAutism is a developmental disorder characterized by impaired social skills and accompanied by motor and perceptual atypicalities. Its etiology is an open question, partly due to the diverse range of associated difficulties. Based on recent observations that individuals with autism are slow in updating perceptual priors, we now hypothesized that motor updating is also slow. Slow motor updating is expected to hamper the ability to synchronize to external events, since asynchronies are corrected sluggishly. Since sensorimotor synchronization is important for social bonding and cooperation, its impairment is expected to impair social skills. To test this hypothesis, we measured paced finger tapping to a metronome in neurotypical, ASD, and dyslexia groups. Dyslexia was assessed as a control group with a non-social neurodevelopmental atypicality. Only the ASD group showed reduced sensorimotor synchronization. Trial-by-trial computational modelling revealed that their ability to form controlled motor responses and to maintain reliable temporal representations was adequate. Only their rate of error-correction was slow and was correlated with the severity of their social difficulties. Taken together, these findings suggest that slow updating in autism contributes to both sloppy sensorimotor performance and difficulties in forming social bonds.SignificanceThe prevalence of autism diagnosis has increased immensely is the last decades. Yet its etiology remains a challenge, partly since the functional relations between characteristic social difficulties, perceptual and motor atypicalities are not understood. Using trial-by-trial computational modelling, we show that a single deficit underlies the poor synchronization of individuals with autism in both static and changing environments. Slow updating, leading to slow online error correction of motor plans, has an immense explanatory power explaining both difficulties in sensorimotor synchronization, and social impairments.
Sex-specific retinal anomalies induced by chronic social stress in mice
Authors: Arsenault E , Lavigne AA , Mansouri S , Francis K , Bittar TP , Quessy F , Abdallah K , Barbeau A , Hébert M , Labonté B 
Published: September 2020

AbstractMajor depressive disorder (MDD) is one of the most common consequences of chronic stress. Still, there is currently no reliable biomarker to detect individuals at risk to develop MDD. Recently, the retina emerged as an effective way to approach the brain and investigate psychiatric disorders with the use of the electroretinogram (ERG). In this study, cones and rods ERGs were performed in male and female mice before and after chronic social defeat stress (CSDS). Mice were then divided as susceptible or resilient to stress. Significant results were only observed in rods ERGs. In males, susceptible mice showed prolonged a-wave implicit times at baseline that were shortened after CSDS. The a-wave was also decreased in both susceptible and resilient male mice after CSDS. In females, rod a-waves were shorter in susceptible than in control mice after CSDS resulting from the latter demonstrating delayed a-waves. Baseline ERGs were able to predict – to some extent – the expression of susceptibility and resilience before stress exposition in male and female mice. Overall, our findings suggest that retinal activity is a presumptive biomarker of stress response and that the ERG could potentially serve as a predicting tool of the stress response in mice.
Synaptic correlates of associative fear memory in the lateral amygdala
Authors: Choi Dong Il , Kim Ji-il , Kim Jooyoung , Lee Hoonwon , Choi Ja Eun , Park Pojeong , Jung Hyunsu , Kaang Bong-Kiun 
Published: September 2020

AbstractSuccessful adaptation to the environment requires accurate responding to external threats by recalling specific memories. However, elucidating underlying neural substrates of associative fear memory was limited due to the difficulties in direct examination of extinction-induced changes of specific synapses that encode an auditory fear memory. Using dual-eGRASP (enhanced Green Fluorescent Protein Reconstitution Across Synaptic Partners), we found that synapses between engram cells or synaptic engram showed a significantly larger spine morphology at auditory cortex (AC) to lateral amygdala (LA) projections after auditory fear conditioning. Fear extinction reversed the enhanced synaptic engram spines while re-conditioning with the same tone and shock restored the size of the synaptic engram. Taken together, we suggest that the synaptic engram may represent a different state of fear memory.One Sentence SummaryAssociative fear memory enlarged the spine morphology of synapses between engram neurons in the amygdala, which was diminished by memory extinction and restored by re-conditioning, suggesting that connections between engram cells represent a different state of fear memory.
Herpes simplex virus entry by a non-conventional endocytic pathway
Authors: Tebaldi Giulia , Pritchard Suzanne M. , Nicola Anthony V. 
Published: September 2020

ABSTRACTHerpes simplex virus 1 (HSV-1) causes significant morbidity and mortality in humans worldwide. HSV-1 enters epithelial cells via an endocytosis mechanism that is low pH-dependent. However, the precise intracellular pathway has not been identified, including the compartment where fusion occurs. In this study, we utilized a combination of molecular and pharmacological approaches to better characterize HSV entry by endocytosis. HSV-1 entry was unaltered in both cells treated with siRNA to Rab5 or Rab7 and cells expressing dominant-negative forms of these GTPases, suggesting entry is independent of the conventional endo-lysosomal network. The fungal metabolite brefeldin A (BFA) and the quinoline compound Golgicide A (GCA) inhibited HSV-1 entry via beta-galactosidase reporter assay and impaired incoming virus transport to the nuclear periphery, suggesting a role for trans Golgi network (TGN) functions and retrograde transport in HSV entry. Silencing of Rab9 or Rab11 GTPases, which are involved in the retrograde transport pathway, resulted in only a slight reduction in HSV infection. Together these results suggest that HSV enters host cells by an intracellular route independent of the lysosome-terminal endocytic pathway.IMPORTANCEHSV-1, the prototype alphaherpesvirus, is ubiquitous in the human population and causes lifelong infection that can be fatal in neonatal and immunocompromised individuals. HSV enters many cell types by endocytosis, including epithelial cells, the site of primary infection in the host. The intracellular itinerary for HSV entry remains unclear. We probed the potential involvement of several Rab GTPases in HSV-1 entry, and suggest that endocytic entry of HSV-1 is independent of the canonical lysosome-terminal pathway. A non-traditional endocytic route may be employed, such as one that intersects with the TGN. These results may lead to novel targets for intervention.
PYMEVisualize: an open-source tool for exploring 3D super-resolution data
Authors: Marin Zach , Graff Michael , Barentine Andrew E. S. , Soeller Christian , Chung Kenny Kwok Hin , Fuentes Lukas A. , Baddeley David 
Published: September 2020

ABSTRACTLocalization-based super-resolution microscopy techniques such as PALM, STORM, and PAINT are increasingly critical tools for biological discovery. These methods generate lists of single fluorophore positions that capture nanoscale structural details of subcellular organisation, but to develop biological insight, we must post-process and visualize this data in a meaningful way. A large number of algorithms have been developed for localization post-processing, transforming point data into representations which approximate traditional microscopy images, and performing specific quantitative analysis directly on points. Implementations of these algorithms typically stand in isolation, necessitating complex workflows involving multiple different software packages. Here we present PYMEVisualize, an open-source tool for the interactive exploration and analysis of 3D, multicolor, single-molecule localization data. PYMEVisualize brings together a broad range of the most commonly used post-processing, density mapping, and direct quantification tools in an easy-to-use and extensible package. This software is one component of the PYthon Microscopy Environment (python-microscopy.org), an integrated application suite for light microscopy acquisition, data storage, visualization, and analysis built on top of the scientific Python environment.