bluuebunny/crossref_metadata_2025_split huggingface dataset:
The course of physical functioning in the first two years after stroke depends on peoples’ individual movement behavior patterns
Authors: Wondergem Roderick , Pisters Martijn F , Wouters Eveline JM , de Bie Rob A , Veenhof Cindy , Visser-Meily Johanna MA 
Published: March 2021

Background and purpose Deterioration of physical functioning after stroke in the long term is regarded as a major problem. Currently, the relationship between “peoples'” movement behavior patterns (the composition of sedentary behavior and physical activity during waking hours) directly after stroke and the development of physical functioning over time is unknown. Therefore, the objectives of this study were to investigate (1) the course of physical functioning within the first two years after returning home after stroke, and (2) the association between physical functioning and baseline movement behavior patterns. Method In the longitudinal RISE cohort study, 200 persons with a first-ever stroke discharged to the home-setting were included. Participants’ physical functioning was assessed within three weeks, at six months, and one and two years after discharge using the Stroke Impact Scale (SIS) 3.0 subscale physical and the five-meter walk test (5MWT). Three distinct movement behavior patterns were identified in a previous study at baseline and were used in the current study: (1) sedentary exercisers (sufficiently active and 64% of waking hours sedentary) , (2) sedentary movers’ (inactive and 63% of waking hours sedentary) , and (3) sedentary prolongers (inactive and >78% of waking hours sedentary accumulated in long prolonged bouts) . The association between movement behavior patterns and the course of physical functioning was determined using longitudinal generalized estimating equations analyses. Results Overall participants’ physical functioning increased between discharge and six months and declined from six months up to two years. Physical functioning remained stable during the first two years after stroke in sedentary exercisers. Physical functioning improved during the first six months after discharge in sedentary movers and sedentary prolongers and deteriorated in the following six months. Only physical functioning (SIS) of sedentary prolongers further declined from one up to two years. A similar pattern was observed in the 5MWT. Conclusion Movement behavior patterns identified directly after returning home in people with stroke are associated with and are predictive of the course of physical functioning. Highly sedentary and inactive people with stroke have unfavorable outcomes over time than individuals with higher amounts of physical activity.
Long-term neurobehavioral correlates of brain cortical microinfarcts in a memory clinic cohort in Singapore
Authors: Xu Xin , Ni Kan Cheuk , Li-Hsian Chen Christopher , Hilal Saima 
Published: March 2021

Background Cortical cerebral microinfarcts are a small vessel disease biomarker underlying cognitive impairment and dementia. However, it is unknown whether cortical cerebral microinfarcts are associated with neuropsychiatric disturbances, and whether its effects are independent of conventional small vessel disease markers. Aims We investigated the associations of cortical cerebral microinfarcts burden with incidence and progression of neuropsychiatric subsyndromes in a memory clinic cohort of elderly in Singapore. Methods In this prospective cohort, 496 subjects underwent detailed neuropsychological and clinical assessments, 3T brain MRI, and Neuropsychiatric Inventory assessment at baseline and two years later. Cortical cerebral microinfarcts and other small vessel disease markers, including white matter hyperintensities, lacunes, and microbleeds, were graded according to established criteria. Neuropsychiatric symptoms (NPS) were clustered into subsyndromes of hyperactivity, psychosis, affective, and apathy following prior findings. Functional decline was determined using the clinical dementia rating (CDR) scale. Results The presence of multiple cortical cerebral microinfarcts (≥2) was associated with higher total NPS scores ( β = 4.19, 95% CI = 2.81–5.58, p < 0.001), particularly hyperactivity ( β = 2.01, 95% CI = 1.30–2.71, p < 0.01) and apathy ( β = 1.42, 95% CI = 0.65–2.18, p < 0.01) at baseline. Between baseline and year-2, multiple cortical cerebral microinfarcts were associated with accelerated progression in total NPS scores ( β = 0.29, 95% CI = 0.06–0.53, p = 0.015), driven by hyperactivity ( β = 0.45, 95% CI = 0.17–0.72, p < 0.01). Subjects with multiple cortical cerebral microinfarcts also had a faster functional decline, as measured with the CDR-sum-of-boxes scores, when accompanied with progression ( β = 0.31, 95% CI = 0.11–0.51, p < 0.01) or hyperactivity in total NPS ( β = 0.34, 95% CI = 0.13–0.56, p < 0.01). Conclusion Cortical cerebral microinfarcts are associated with incidence and progression of geriatric neurobehavioral disturbances, independent of conventional small vessel disease markers. The impact of incident cortical cerebral microinfarcts on neurocognitive and neuropsychiatric trajectories warrants further investigations.
Associations between dysbiosis-inducing drugs, overall survival and tumor response in patients treated with immune checkpoint inhibitors
Authors: Gaucher Louis , Adda Leslie , Séjourné Alice , Joachim Camille , Guillaume Chaby , Poulet Claire , Liabeuf Sophie , Gras-Champel Valérie , Masmoudi Kamel , Houessinon Aline , Bennis Youssef , Batteux Benjamin 
Published: March 2021

Background: There are conflicting data on the effects of dysbiosis-inducing drugs, and especially antibiotics (ATBs), on clinical outcomes in patients treated with immune checkpoint inhibitors (ICIs). There is a particular lack of data for patients with melanoma. Methods: We performed a single-center retrospective study of the associations between ATBs and other drugs known to modify the gut microbiota (proton pump inhibitors, nonsteroidal anti-inflammatory drugs, statins, opioids, anti-vitamin K, levothyroxine, vitamin D3, antiarrhythmics, metformin and phloroglucinol), overall survival (OS) and tumor response in consecutive cancer patients (particularly those with melanoma) treated with an ICI (ipilimumab, nivolumab or pembrolizumab) over a 9-year period. Results: A total of 372 patients were included. The mean ± standard deviation age was 64.0 ± 12.1 years. The most frequently prescribed ICI was nivolumab (in 58.3% of patients) and the most frequent indications were lung cancer (44.6%) and melanoma (29.6%). Overall, 112 patients (30.1%) had received ATBs. ATB use was associated with (1) shorter OS in the study population as a whole [adjusted hazard ratio [95% confidence interval (CI)]: 1.38 (1.00–1.90), p = 0.048] and in patients with melanoma [adjusted hazard ratio (95% CI): 2.60 (1.06–6.39), p = 0.037], and (2) a lower response rate in the study population as a whole [8.1%, versus 31.1% in patients not treated with ATBs; adjusted odds ratio (95% CI): 6.06 (2.80–14.53), p < 0.001] and in patients with melanoma [adjusted odds ratio (95% CI): 4.41 (1.04–22.80), p = 0.045]. Sensitivity analyses that minimized the indication bias did not reveal an association between OS and the presence of an infection requiring ATBs (quantified as the severity of infection, hospitalization for an infection, or ICI discontinuation). Other dysbiosis-inducing drugs were not associated with a difference in OS. Conclusion: Unlike other dysbiosis-inducing drugs, ATBs were associated with poorer clinical outcomes in ICI-treated patients overall and in the subset of patients with melanoma.
Health Disparities in Calorie Knowledge and Confidence Among the U.S. Adult Population
Authors: Lando Amy M. , Ferguson Martine S. , Verrill Linda , Wu Fanfan , Jones-Dominic Olivia E. , Punzalan Cecile , Wolpert Beverly J. 
Published: March 2021

Purpose Obesity prevalence has reached an all-time high in the US, affecting >40% of the population. This study’s objective was to evaluate associations between demographics and self-reported calorie knowledge and self-perceived confidence in calorie knowledge (“calorie confidence”). The relationships between body mass index (BMI) and calorie knowledge and confidence were also explored. Methods We analyzed data from participants (n = 2171) in the crosssectional, nationally representative 2019 FDA Food Safety and Nutrition Survey using logistic regression to estimate adjusted odds ratios (AORs) and confidence intervals (95% CIs) for associations between BMI and calorie knowledge (correct/incorrect), calorie confidence (confident/not confident), and demographic characteristics, and the Wald chi square test to evaluate relationships between BMI and both calorie knowledge and confidence. Results Many of the same subgroups were more likely than others to report lack of calorie knowledge and lack of confidence in knowing the typical daily calorie intake needed to maintain a healthy weight [respective AORs (95% CIs): age (years), >60 vs 51-60, 1.7 (1.1-2.5), and 1.4 (1.0-2.0); sex, male vs female, 1.7 (1.3-2.3), and 1.7 (1.3-2.1); race/ethnicity, non-Hispanic Black vs non-Hispanic white, 3.4 (2.1-5.5), and 2.4 (1.6-3.8); education, ≤high school vs college grad, 1.5 (1.0- 2.3), and 1.9 (1.3-2.7)]. BMI was significantly correlated with calorie confidence ( P = .047), such that those reporting less confidence were more likely overweight or obese [underweight/healthy (BMI < 25): 29%, overweight (25 ≤ BMI < 30): 34%, obese (BMI ≥ 30): 37%]. Conclusion In certain demographic subgroups associations between calorie knowledge and confidence differed. Tailored education and outreach for these groups may help to address these disparities.
Clustering and prioritization to design a risk-based monitoring program in groundwater sources for drinking water
Authors: Sjerps Rosa M. A. , Brunner Andrea M. , Fujita Yuki , Bajema Bernard , de Jonge Martin , Bäuerlein Patrick S. , de Munk Joost , Schriks Merijn , van Wezel Annemarie 
Published: March 2021

Abstract
Background
The number of chemical parameters included in monitoring programs of water utilities increased in the last decade. In accordance with the European Drinking Water Directive, utilities aim at a tailored risk-based monitoring (RBM) program. Here, such a RBM program was developed for the largest Dutch water utility, mostly using groundwater as a source. Data from target analyses and high-resolution mass spectrometry-based suspect screening was used to cluster the different source waters. Targets were prioritized based on (preliminary) drinking water guideline values or the threshold of toxicological concern. Suspects were prioritized for further identity confirmation based on semi-quantitative occurrence concentrations combined with in vitro toxicity information. Finally, a RBM program was suggested for each cluster of source waters.

Results
Out of 731 target chemicals, 153 were detected at least once over a 5-year period. Roughly 10% of the detected non-target screening features matched to suspects. 108 source waters were clustered into 7 clusters. Source waters with low numbers and concentrations of organic chemicals were located in areas with all land-use types, while clusters of source waters with higher numbers of chemicals were related to infiltrated surface water. For perfluorinated chemicals, 25 suspects matched features detected in source waters and 7 features detected in drinking water. For the target chemicals, simple treatment showed the lowest and sorption-based techniques relatively high removal efficiencies. The chemical composition of all drinking waters related to non-contaminated source waters. (Preliminary) guideline values were available for 45 of the retrieved target chemicals, and used for prioritization for monitoring frequencies. These chemicals individually posed no appreciable concern to human health. Suspects were prioritized for further identity confirmation based on semi-quantitative occurrence in produced water, detection frequencies and information on toxic potency. Once confirmed and assessed as relevant, the suspects could be added to target monitoring.

Conclusion
This approach provided a feasible workflow for RBM of target chemicals for clusters of groundwater sources, connected to a feed of new relevant chemicals based on suspect screening.
Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference
Authors: Spillane Jennifer L. , LaPolice Troy M. , MacManes Matthew D. , Plachetzki David C. 
Published: March 2021

Abstract
Background
Phylogenomic approaches have great power to reconstruct evolutionary histories, however they rely on multi-step processes in which each stage has the potential to affect the accuracy of the final result. Many studies have empirically tested and established methodology for resolving robust phylogenies, including selecting appropriate evolutionary models, identifying orthologs, or isolating partitions with strong phylogenetic signal. However, few have investigated errors that may be initiated at earlier stages of the analysis. Biases introduced during the generation of the phylogenomic dataset itself could produce downstream effects on analyses of evolutionary history. Transcriptomes are widely used in phylogenomics studies, though there is little understanding of how a poor-quality assembly of these datasets could impact the accuracy of phylogenomic hypotheses. Here we examined how transcriptome assembly quality affects phylogenomic inferences by creating independent datasets from the same input data representing high-quality and low-quality transcriptome assembly outcomes.

Results
By studying the performance of phylogenomic datasets derived from alternative high- and low-quality assembly inputs in a controlled experiment, we show that high-quality transcriptomes produce richer phylogenomic datasets with a greater number of unique partitions than low-quality assemblies. High-quality assemblies also give rise to partitions that have lower alignment ambiguity and less compositional bias. In addition, high-quality partitions hold stronger phylogenetic signal than their low-quality transcriptome assembly counterparts in both concatenation- and coalescent-based analyses.

Conclusions
Our findings demonstrate the importance of transcriptome assembly quality in phylogenomic analyses and suggest that a portion of the uncertainty observed in such studies could be alleviated at the assembly stage.
A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum
Authors: Podio Maricel , Colono Carolina , Siena Lorena , Ortiz Juan Pablo A. , Pessino Silvina Claudia 
Published: March 2021

Abstract
Background
Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of maternal seeds. Recently, reference floral transcriptomes were generated from sexual and apomictic biotypes of Paspalum notatum, one of the most well-known plant models for the study of apomixis. However, the transcriptome dynamics, the occurrence of apomixis vs. sexual expression heterochronicity across consecutive developmental steps and the orientation of transcription (sense/antisense) remain unexplored.

Results
We produced 24 Illumina TruSeq®/ Hiseq 1500 sense/antisense floral transcriptome libraries covering four developmental stages (premeiosis, meiosis, postmeiosis, and anthesis) in biological triplicates, from an obligate apomictic and a full sexual genotype. De novo assemblies with Trinity yielded 103,699 and 100,114 transcripts for the apomictic and sexual samples respectively. A global comparative analysis involving reads from all developmental stages revealed 19,352 differentially expressed sense transcripts, of which 13,205 (68%) and 6147 (32%) were up- and down-regulated in apomictic samples with respect to the sexual ones. Interestingly, 100 differentially expressed antisense transcripts were detected, 55 (55%) of them up- and 45 (45%) down-regulated in apomictic libraries. A stage-by-stage comparative analysis showed a higher number of differentially expressed candidates due to heterochronicity discrimination: the highest number of differential sense transcripts was detected at premeiosis (23,651), followed by meiosis (22,830), postmeiosis (19,100), and anthesis (17,962), while the highest number of differential antisense transcripts were detected at anthesis (495), followed by postmeiosis (164), meiosis (120) and premeiosis (115). Members of the AP2, ARF, MYB and WRKY transcription factor families, as well as the auxin, jasmonate and cytokinin plant hormone families appeared broadly deregulated. Moreover, the chronological expression profile of several well-characterized apomixis controllers was examined in detail.

Conclusions
This work provides a quantitative sense/antisense gene expression catalogue covering several subsequent reproductive developmental stages from premeiosis to anthesis for apomictic and sexual P. notatum, with potential to reveal heterochronic expression between reproductive types and discover sense/antisense mediated regulation. We detected a contrasting transcriptional and hormonal control in apomixis and sexuality as well as specific sense/antisense modulation occurring at the onset of parthenogenesis.
Genomic imprinted genes in reciprocal hybrid endosperm of Brassica napus
Authors: Rong Hao , Yang Wenjing , Zhu Haotian , Jiang Bo , Jiang Jinjin , Wang Youping 
Published: March 2021

AbstractBackgroundGenomic imprinting results in the expression of parent-of-origin-specific alleles in the offspring.Brassica napusis an oil crop with research values in polyploidization. Identification of imprinted genes inB. napuswill enrich the knowledge of genomic imprinting in dicotyledon plants.ResultsIn this study, we performed reciprocal crosses betweenB. napusL. cultivars Yangyou 6 (Y6) and Zhongshuang 11 (ZS11) to collect endosperm at 20 and 25 days after pollination (DAP) for RNA-seq. In total, we identified 297 imprinted genes, including 283 maternal expressed genes (MEGs) and 14 paternal expressed genes (PEGs) according to the SNPs between Y6 and ZS11. Only 36 genes (35 MEGs and 1 PEG) were continuously imprinted in 20 and 25 DAP endosperm. We found 15, 2, 5, 3, 10, and 25 imprinted genes in this study were also imprinted inArabidopsis, rice, castor bean, maize,B. rapa, and otherB. napuslines, respectively. Only 26 imprinted genes were specifically expressed in endosperm, while other genes were also expressed in root, stem, leaf and flower bud ofB. napus. A total of 109 imprinted genes were clustered on rapeseed chromosomes. We found the LTR/Copia transposable elements (TEs) were most enriched in both upstream and downstream of the imprinted genes, and the TEs enriched around imprinted genes were more than non-imprinted genes. Moreover, the expression of 5AGLsand 6 pectin-related genes in hybrid endosperm were significantly changed comparing with that in parent endosperm.ConclusionThis research provided a comprehensive identification of imprinted genes inB. napus, and enriched the gene imprinting in dicotyledon plants, which would be useful in further researches on how gene imprinting regulates seed development.
Chromosome behavior during meiosis in pollen mother cells from Saccharum officinarum × Erianthus arundinaceus F1 hybrids
Authors: Li Xueting , Huang Fei , Chai Jin , Wang Qiusong , Yu Fan , Huang Yongji , Wu Jiayun , Wang Qinnan , Xu Liangnian , Zhang Muqing , Deng Zuhu 
Published: March 2021

Abstract
Background
In recent years, sugarcane has attracted increasing attention as an energy crop. Wild resources are widely used to improve the narrow genetic base of sugarcane. However, the infertility of F1 hybrids between Saccharum officinarum (S. officinarum) and Erianthus arundinaceus (E. arundinaceus) has hindered sugarcane breeding efforts. To discover the cause of this infertility, we studied the hybridization process from a cytological perspective.

Results
We examined the meiotic process of pollen mother cells (PMCs) in three F1 hybrids between S. officinarum and E. arundinaceus. Cytological analysis showed that the male parents, Hainan 92–77 and Hainan 92–105, had normal meiosis. However, the meiosis process in F1 hybrids showed various abnormal phenomena, including lagging chromosomes, micronuclei, uneven segregation, chromosome bridges, and inability to form cell plates. Genomic in situ hybridization (GISH) showed unequal chromatin distribution during cell division. Interestingly, 96.70% of lagging chromosomes were from E. arundinaceus. Furthermore, fluorescence in situ hybridization (FISH) was performed using 45S rDNA and 5S rDNA as probes. Either 45S rDNA or 5S rDNA sites were lost during abnormal meiosis, and results of unequal chromosomal separation were also clearly observed in tetrads.

Conclusions
Using cytogenetic analysis, a large number of meiotic abnormalities were observed in F1. GISH further confirmed that 96.70% of the lagging chromosomes were from E. arundinaceus. Chromosome loss was found by further investigation of repeat sequences. Our findings provide insight into sugarcane chromosome inheritance to aid innovation and utilization in sugarcane germplasm resources.
A next-generation sequencing-based strategy combining microsatellite instability and tumor mutation burden for comprehensive molecular diagnosis of advanced colorectal cancer
Authors: Xiao Jian , Li Wenyun , Huang Yan , Huang Mengli , Li Shanshan , Zhai Xiaohui , Zhao Jing , Gao Chan , Xie Wenzhuan , Qin Hao , Cai Shangli , Bai Yuezong , Lan Ping , Zou Yifeng 
Published: March 2021

Abstract
Background
Mismatch repair (MMR)/microsatellite instability (MSI) and tumor mutational burden (TMB) are independent biomarkers that complement each other for predicting immune checkpoint inhibitors (ICIs) efficacy. Here we aim to establish a strategy that integrates MSI and TMB determination for colorectal cancer (CRC) in one single assay.

Methods
Surgical or biopsy specimens retrospectively collected from CRC patients were subjected to NGS analysis. Immunohistochemistry (IHC) and polymerase chain reaction (PCR) were also used to determine MMR/MSI for those having enough tissues. The NGS-MSI method was validated against IHC and PCR. The MSI-high (MSI-H) or microsatellite stable (MSS) groups were further stratified based on tumor mutational burden, followed by validation using the The Cancer Genome Atlas (TCGA) CRC dataset. Immune microenvironment was evaluated for each subgroup be profiling the expression of immune signatures.

Results
Tissues from 430 CRC patients were analyzed using a 381-gene NGS panel. Alterations in KRAS, NRAS, BRAF, and HER2 occurred at a significantly higher incidence among MSI-H tumors than in MSS patients (83.6% vs. 58.4%, p = 0.0003). A subset comprising 98 tumors were tested for MSI/MMR using all three techniques, where NGS proved to be 99.0 and 93.9% concordant with PCR and IHC, respectively. Four of the 7 IHC-PCR discordant cases had low TMB (1.1–8.1 muts/Mb) and were confirmed to have been misdiagnosed by IHC. Intriguingly, 4 of the 66 MSS tumors (as determined by NGS) were defined as TMB-high (TMB-H) using a cut-off of 29 mut/Mb. Likewise, 15 of the 456 MSS tumors in the TCGA CRC cohort were also TMB-H with a cut-off of 9 muts/Mb. Expression of immune signatures across subgroups (MSS-TMB-H, MSI-H-TMB-H, and MSS-TMB-L) confirmed that the microenvironment of the MSS-TMB-H tumors was similar to that of the MSI-H-TMB-H tumors, but significantly more immune-responsive than that of the MSS-TMB-L tumors, indicating that MSI combined with TMB may be more precise than MSI alone for immune microenvironment prediction.

Conclusion
This study demonstrated that NGS panel-based method is both robust and tissue-efficient for comprehensive molecular diagnosis of CRC. It also underscores the importance of combining MSI and TMB information for discerning patients with different microenvironment.