bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resting State Connectivity Is Modulated by Motor Learning in Individuals After Stroke
Authors: Kraeutner Sarah N. , Rubino Cristina , Rinat Shie , Lakhani Bimal , Borich Michael R. , Wadden Katie P. , Boyd Lara A. 
Published: April 2021

Objective Activity patterns across brain regions that can be characterized at rest (ie, resting-state functional connectivity [rsFC]) are disrupted after stroke and linked to impairments in motor function. While changes in rsFC are associated with motor recovery, it is not clear how rsFC is modulated by skilled motor practice used to promote recovery. The current study examined how rsFC is modulated by skilled motor practice after stroke and how changes in rsFC are linked to motor learning. Methods Two groups of participants (individuals with stroke and age-matched controls) engaged in 4 weeks of skilled motor practice of a complex, gamified reaching task. Clinical assessments of motor function and impairment, and brain activity (via functional magnetic resonance imaging) were obtained before and after training. Results While no differences in rsFC were observed in the control group, increased connectivity was observed in the sensorimotor network, linked to learning in the stroke group. Relative to healthy controls, a decrease in network efficiency was observed in the stroke group following training. Conclusions Findings indicate that rsFC patterns related to learning observed after stroke reflect a shift toward a compensatory network configuration characterized by decreased network efficiency.
Preoperative hematocrit and platelet count are associated with blood loss during spinal fusion for children with neuromuscular scoliosis
Authors: Lewen Margaret O , Berry Jay , Johnson Connor , Grace Rachael , Glader Laurie , Crofton Charis , Leahy Izabela , Pallikonda Nikhil , Litvinova Anna , Staffa Steven J , Glotzbecker Michael , Emans John , Hresko M Timothy , Ellen Mary , Troy Michael , Singer Sara J , Ferrari Lynne 
Published: April 2021

Aim To assess the relationship of preoperative hematology laboratory results with intraoperative estimated blood loss and transfusion volumes during posterior spinal fusion for pediatric neuromuscular scoliosis. Methods Retrospective chart review of 179 children with neuromuscular scoliosis undergoing spinal fusion at a tertiary children’s hospital between 2012 and 2017. The main outcome measure was estimated blood loss. Secondary outcomes were volumes of packed red blood cells, fresh frozen plasma, and platelets transfused intraoperatively. Independent variables were preoperative blood counts, coagulation studies, and demographic and surgical characteristics. Relationships between estimated blood loss, transfusion volumes, and independent variables were assessed using bivariable analyses. Classification and Regression Trees were used to identify variables most strongly correlated with outcomes. Results In bivariable analyses, increased estimated blood loss was significantly associated with higher preoperative hematocrit and lower preoperative platelet count but not with abnormal coagulation studies. Preoperative laboratory results were not associated with intraoperative transfusion volumes. In Classification and Regression Trees analysis, binary splits associated with the largest increase in estimated blood loss were hematocrit ≥44% vs. <44% and platelets ≥308 vs. <308 × 109/L. Conclusions Preoperative blood counts may identify patients at risk of increased bleeding, though do not predict intraoperative transfusion requirements. Abnormal coagulation studies often prompted preoperative intervention but were not associated with increased intraoperative bleeding or transfusion needs.
Amide proton transfer imaging for differentiation of tuberculomas from high-grade gliomas: Preliminary experience
Authors: Kulanthaivelu Karthik , Jabeen Shumyla , Saini Jitender , Raju Sanita , Nalini Atchayaram , Sadashiva Nishanth , Hegde Shashank , Rolla Narayana Krishna , Saha Indrajit , M Netravathi , Vengalil Seena , Swaroop Saikrishna , Rao Shilpa 
Published: April 2021

Purpose Tuberculomas can occasionally masquerade as high-grade gliomas (HGG). Evidence from magnetisation transfer (MT) imaging suggests that there is lower protein content in the tuberculoma microenvironment. Building on the principles of chemical exchange saturation transfer and MT, amide proton transfer (APT) imaging generates tissue contrast as a function of the mobile amide protons in tissue’s native peptides and intracellular proteins. This study aimed to further the understanding of tuberculomas using APT and to compare it with HGG. Method Twenty-two patients ( n = 8 tuberculoma; n = 14 HGG) were included in the study. APT was a 3D turbo spin-echo Dixon sequence with inbuilt B0 correction. A two-second, 2 μT saturation pulse alternating over transmit channels was applied at ±3.5 ppm around water resonance. The APT-weighted image (APTw) was computed as the MT ratio asymmetry (MTRasym) at 3.5 ppm. Mean MTRasym values in regions of interest (areas = 9 mm2; positioned in component with homogeneous enhancement/least apparent diffusion coefficient) were used for the analysis. Results MTRasym values of tuberculomas ( n = 14; 8 cases) ranged from 1.34% to 3.11% ( M = 2.32 ± 0.50). HGG ( n = 17;14 cases) showed MTRasym ranging from 2.40% to 5.70% ( M = 4.32 ± 0.84). The inter-group difference in MTRasym was statistically significant ( p < 0.001). APTw images in tuberculomas were notable for high MTRasym values in the perilesional oedematous-appearing parenchyma (compared to contralateral white matter; p < 0.001). Conclusion Tuberculomas demonstrate lower MTRasym ratios compared to HGG, reflective of a relative paucity of mobile amide protons in the ambient microenvironment. Elevated MTRasym values in perilesional parenchyma in tuberculomas are a unique observation that may be a clue to the inflammatory milieu.
Association Between Osteochondritis Dissecans of the Humeral Capitellum and Medial Epicondyle Lesion in Baseball Players
Authors: Kamei Keita , Sasaki Norihiro , Sasaki Eiji , Sasaki Shizuka , Kimura Yuka , Maeda Shugo , Yamamoto Yuji , Ishibashi Yasuyuki 
Published: April 2021

Background: Osteochondritis dissecans (OCD) of the humeral capitellum occurs in adolescent overhead athletes, and medial epicondyle (ME) lesions are also common in this population. Purpose: To evaluate the association between elbow OCD and ME lesions in adolescent baseball players. Study Design: Cross-sectional study; Level of evidence, 3. Methods: This study retrospectively evaluated adolescent baseball players with unstable elbow OCD who underwent surgery between January 2000 and February 2020. Patients were excluded if they had osteoarthritis of the elbow. A total of 139 elbows were included in this study (138 male and 1 female athlete; mean ± SD age, 13.6 ± 1.5 years). The patients were first divided into 2 groups based on OCD location: a central lesion group (72 elbows) and a lateral group (67 elbows). Next, patients were divided according to OCD size into a localized group (56 elbows) and a widespread group (83 elbows). Finally, OCD lesions that were both lateral and widespread were defined as lateral-widespread (60 elbows), resulting in 5 groups. ME apophyseal fragmentation and elongation were evaluated and defined as ME lesions. We then compared the relationship between OCD and ME lesions. Results: Of the 139 elbows, 63 (45.3%) had ME lesions. The prevalence of ME lesion was higher in the lateral group than the central group (56.7% vs 34.7%; P = .009) and higher in the widespread group than the localized group (55.4% vs 30.4%; P = .004). Furthermore, the prevalence ratio of ME lesion was significantly higher in the lateral-widespread group than for other lesions (58.3% vs 35.4%; P = .007). Conclusion: In patients undergoing surgery for capitellar OCD, the presence of ME lesions was more commonly associated with lateral and widespread capitellar lesions when compared with central and localized lesions.
Hepatocyte neogenin is required for hemojuvelin-mediated hepcidin expression and iron homeostasis in mice
Authors: Enns Caroline A. , Jue Shall , Zhang An-Sheng 
Published: April 2021

Abstract
Neogenin (NEO1) is a ubiquitously expressed multifunctional transmembrane protein. It interacts with hemojuvelin (HJV), a BMP coreceptor that plays a pivotal role in hepatic hepcidin expression. Earlier studies suggest that the function of HJV relies on its interaction with NEO1. However, the role of NEO1 in iron homeostasis remains controversial because of the lack of an appropriate animal model. Here, we generated a hepatocyte-specific Neo1 knockout (Neo1fl/fl;Alb-Cre+) mouse model that circumvented the developmental and lethality issues of the global Neo1 mutant. Results show that ablation of hepatocyte Neo1 decreased hepcidin expression and caused iron overload. This iron overload did not result from altered iron utilization by erythropoiesis. Replacement studies revealed that expression of the Neo1L1046E mutant that does not interact with Hjv, was unable to correct the decreased hepcidin expression and high serum iron in Neo1fl/fl;Alb-Cre+ mice. In Hjv−/− mice, expression of HjvA183R mutant that has reduced interaction with Neo1, also displayed a blunted induction of hepcidin expression. These observations indicate that Neo1-Hjv interaction is essential for hepcidin expression. Further analyses suggest that the Hjv binding triggered the cleavage of the Neo1 cytoplasmic domain by a protease, which resulted in accumulation of truncated Neo1 on the plasma membrane. Additional studies did not support that Neo1 functions by inhibiting Hjv shedding as previously proposed. Together, our data favor a model in which Neo1 interaction with Hjv leads to accumulation of cleaved Neo1 on the plasma membrane, where Neo1 acts as a scaffold to induce the Bmp signaling and hepcidin expression.
Intact TP-53 function is essential for sustaining durable responses to BH3-mimetic drugs in leukemias
Authors: Thijssen Rachel , Diepstraten Sarah T. , Moujalled Donia , Chew Edward , Flensburg Christoffer , Shi Melissa X. , Dengler Michael A. , Litalien Veronique , MacRaild Sarah , Chen Maoshan , Anstee Natasha S. , Reljić Boris , Gabriel Sarah S. , Djajawi Tirta M. , Riffkin Chris D. , Aubrey Brandon J. , Chang Catherine , Tai Lin , Xu Zhen , Morley Thomas , Pomilio Giovanna , Bruedigam Claudia , Kallies Axel , Stroud David A. , Bajel Ashish , Kluck Ruth M. , Lane Steven W. , Schoumacher Marie , Banquet Sébastien , Majewski Ian J. , Strasser Andreas , Roberts Andrew W. , Huang David C. S. , Brown Fiona C. , Kelly Gemma L. , Wei Andrew H. 
Published: April 2021

AbstractSelective targeting of BCL-2 with the BH3-mimetic venetoclax has been a transformative treatment for patients with various leukemias. TP-53 controls apoptosis upstream of where BCL-2 and its prosurvival relatives, such as MCL-1, act. Therefore, targeting these prosurvival proteins could trigger apoptosis across diverse blood cancers, irrespective of TP53 mutation status. Indeed, targeting BCL-2 has produced clinically relevant responses in blood cancers with aberrant TP-53. However, in our study, TP53-mutated or -deficient myeloid and lymphoid leukemias outcompeted isogenic controls with intact TP-53, unless sufficient concentrations of BH3-mimetics targeting BCL-2 or MCL-1 were applied. Strikingly, tumor cells with TP-53 dysfunction escaped and thrived over time if inhibition of BCL-2 or MCL-1 was sublethal, in part because of an increased threshold for BAX/BAK activation in these cells. Our study revealed the key role of TP-53 in shaping long-term responses to BH3-mimetic drugs and reconciled the disparate pattern of initial clinical response to venetoclax, followed by subsequent treatment failure among patients with TP53-mutant chronic lymphocytic leukemia or acute myeloid leukemia. In contrast to BH3-mimetics targeting just BCL-2 or MCL-1 at doses that are individually sublethal, a combined BH3-mimetic approach targeting both prosurvival proteins enhanced lethality and durably suppressed the leukemia burden, regardless of TP53 mutation status. Our findings highlight the importance of using sufficiently lethal treatment strategies to maximize outcomes of patients with TP53-mutant disease. In addition, our findings caution against use of sublethal BH3-mimetic drug regimens that may enhance the risk of disease progression driven by emergent TP53-mutant clones.
SPL36 Encodes a Receptor-like Protein Kinase that Regulates Programmed Cell Death and Defense Responses in Rice
Authors: Yuchun R. A. O. , Ran J. I. A. O. , Sheng W. A. N. G. , Xianmei W. U. , Hanfei Y. E. , Chenyang P. A. N. , Sanfeng L. I. , Dedong Xin , Weiyong Z. H. O. U. , Gaoxing D. A. I. , Juan H. U. , Deyong R. E. N. , Yuexing W. A. N. G. 
Published: April 2021

AbstractLesion mimic mutants spontaneously produce disease spots in the absence of biotic or abiotic stresses. Analyzing lesion mimic mutants’ sheds light on the mechanisms underlying programmed cell death and defense-related responses in plants. Here, we isolated and characterized the rice (Oryza sativa) spotted leaf 36 (spl36) mutant, which was identified from an ethyl methanesulfonate-mutagenized japonica cultivar Yundao population. spl36 displayed spontaneous cell death and enhanced resistance to rice bacterial pathogens. Gene expression analysis suggested that spl36 functions in the disease response by upregulating the expression of defense-related genes. Physiological and biochemical experiments indicated that more cell death occurred in spl36 than the wild type and that plant growth and development were affected in this mutant. We isolated SPL36 by map-based cloning. A single base substitution was detected in spl36, which results in a cysteine-to-arginine substitution in SPL36. SPL36 is predicted to encode a receptor-like protein kinase containing leucine-rich domains that may be involved in stress responses in rice. spl36 was more sensitive to salt stress than the wild type, suggesting that SPL36 also negatively regulates the salt-stress response. These findings suggest that SPL36 regulates the disease resistance response in rice by affecting the expression of defense- and stress-related genes.
Comparing the outcome of ileal conduit and transuretero-cutaneostomy urinary diversion after radical cystectomy: a retrospective cohort study
Authors: Khalilullah Said Alfin , Tranggono Untung , Hendri Ahmad Zulfan , Danarto R. 
Published: April 2021

Abstract
Background
Most of the outcomes after radical cystectomy (RC) are directly associated with the type of urinary diversion. This study sets out to evaluate the outcomes of ileal conduit (IC) and transuretero-cutaneostomy (TUC) urinary diversion after RC.

Methods
This retrospective study included 52 patients (IC, n = 30; TUC, n = 22) at Dr. Sardjito Hospital between January 2014 and December 2019. The clinical outcomes were compared using Chi-squared tests and independent t tests. Multivariable logistic regression analysis was performed to determine the odds of developing related complications.

Results
Demographically, both groups were similar in terms of age, gender, ASA score, staging, body mass index, and comorbidities. IC was associated with a high incidence of postoperative complications than TUC (56.7% vs. 27.3%; p = 0.035). Long-term postoperative complications stoma stenosis was more common in the TUC than IC (p = 0.010). Multivariate analysis showed TUC was a significant predictor for stoma stenotic with odds ratio of 1.29 (95% confidence interval, 1.03–1.62; p = 0.006). Meanwhile, metabolic change was found higher in IC (p = 0.047). No difference between the rate of required blood transfusion, postoperative ileus, re-operation, and anastomotic stricture in both groups. Operative time (p = 0.000) and length of stay (p = 0.002) were lower in patients who underwent TUC. The hospitalized cost was also lower in TUC ($ 2311.8 ± 1448 for IC vs. $ 1844.2 ± 948.8 for TUC; p = 0.005). Nonetheless, the follow-up cost was higher in the TUC but not statistically significant. Additionally, there was no difference between the overall satisfaction and diversion-related symptoms scores in both groups. The psychological score was better in IC groups.

Conclusions
Both of these techniques can be an option in a urinary diversion after RC with various advantages and disadvantages. TUC provides reduced complication rates, operative time, shorter length of stay, and hospitalized costs, but IC may reduce postoperative stoma stenosis complications and better psychological function.
EzMAP: Easy Microbiome Analysis Platform
Authors: Shanmugam Gnanendra , Lee Song Hee , Jeon Junhyun 
Published: April 2021

Abstract
Background
The rapid advances in next-generation sequencing technologies have revolutionized the microbiome research by greatly increasing our ability to understand diversity of microbes in a given sample. Over the past decade, several computational pipelines have been developed to efficiently process and annotate these microbiome data. However, most of these pipelines require an implementation of additional tools for downstream analyses as well as advanced programming skills.

Results
Here we introduce a user-friendly microbiome analysis platform, EzMAP (Easy Microbiome Analysis Platform), which was developed using Java Swings, Java Script and R programming language. EzMAP is a standalone package providing graphical user interface, enabling easy access to all the functionalities of QIIME2 (Quantitative Insights Into Microbial Ecology) as well as streamlined downstream analyses using QIIME2 output as input. This platform is designed to give users the detailed reports and the intermediate output files that are generated progressively. The users are allowed to download the features/OTU table (.biom;.tsv;.xls), representative sequences (.fasta) and phylogenetic tree (.nwk), taxonomy assignment file (optional). For downstream analyses, users are allowed to perform relative abundances (at all taxonomical levels), community comparison (alpha and beta diversity, core microbiome), differential abundances (DESeq2 and linear discriminant analysis) and functional prediction (PICRust, Tax4Fun and FunGuilds). Our case study using a published rice microbiome dataset demonstrates intuitive user interface and great accessibility of the EzMAP.

Conclusions
This EzMAP allows users to consolidate the microbiome analysis processes from raw sequence processing to downstream analyses specific for individual projects. We believe that this will be an invaluable tool for the beginners in their microbiome data analysis. This platform is freely available at https://github.com/gnanibioinfo/EzMAP and will be continually updated for adoption of changes in methods and approaches.
Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA
Authors: Park Cooper J. , Caimi Nicole A. , Buecher Debbie C. , Valdez Ernest W. , Northup Diana E. , Andam Cheryl P. 
Published: April 2021

Abstract
Background
Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates.

Results
We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species.

Conclusions
Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.
Transcriptomic analysis of the poultry red mite, Dermanyssus gallinae, across all stages of the lifecycle
Authors: Bartley Kathryn , Chen Wan , Lloyd Mills Richard I. , Nunn Francesca , Price Daniel R. G. , Rombauts Stephane , Van de Peer Yves , Roy Lise , Nisbet Alasdair J. , Burgess Stewart T. G. 
Published: April 2021

AbstractBackgroundThe blood feeding poultry red mite (PRM),Dermanyssus gallinae, causes substantial economic damage to the egg laying industry worldwide, and is a serious welfare concern for laying hens and poultry house workers. In this study we have investigated the temporal gene expression across the 6 stages/sexes (egg, larvae, protonymph and deutonymph, adult male and adult female) of this neglected parasite in order to understand the temporal expression associated with development, parasitic lifestyle, reproduction and allergen expression.ResultsRNA-seq transcript data for the 6 stages were mapped to the PRM genome creating a publicly available gene expression atlas (on the OrcAE platform in conjunction with the PRM genome). Network analysis and clustering of stage-enriched gene expression in PRM resulted in 17 superclusters with stage-specific or multi-stage expression profiles. The 6 stage specific superclusters were clearly demarked from each other and the adult female supercluster contained the most stage specific transcripts (2725), whilst the protonymph supercluster the fewest (165). Fifteen pairwise comparisons performed between the different stages resulted in a total of 6025 Differentially Expressed Genes (DEGs) (P > 0.99). These data were evaluated alongside a Venn/Euler analysis of the top 100 most abundant genes in each stage. An expanded set of cuticle proteins and enzymes (chitinase and metallocarboxypeptidases) were identified in larvae and underpin cuticle formation and ecdysis to the protonymph stage. Two mucin/peritrophic-A salivary proteins (DEGAL6771g00070, DEGAL6824g00220) were highly expressed in the blood-feeding stages, indicating peritrophic membrane formation during feeding. Reproduction-associated vitellogenins were the most abundant transcripts in adult females whilst, in adult males, an expanded set of serine and cysteine proteinases and an epididymal protein (DEGAL6668g00010) were highly abundant. Assessment of the expression patterns of putative homologues of 32 allergen groups from house dust mites indicated a bias in their expression towards the non-feeding larval stage of PRM.ConclusionsThis study is the first evaluation of temporal gene expression across all stages of PRM and has provided insight into developmental, feeding, reproduction and survival strategies employed by this mite. The publicly available PRM resource on OrcAE offers a valuable tool for researchers investigating the biology and novel interventions of this parasite.