Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatiotemporally Varying Coefficients (STVC) model: a Bayesian local regression to detect spatial and temporal nonstationarity in variables relationships

ABSTRACT Local regression has an advantage over global regression by allowing coefficients that qualify variables relationships being heterogeneous, where such varying regression relationships are nonstationarity. Spatiotemporally Varying Coefficients (STVC) model is the first Bayesian-based local spatiotemporal regression approach, intending to simultaneously detect spatial and temporal nonstationarity for heterogeneous response-covariate variables relationships, through separately estimating posterior local-scale coefficients over different space areas and time frames. In this paper, we first presented a general Bayesian STVC modelling paradigm as a specification guide to show its commonality in broader geospatial research. Then, we employed it to solve a real-world issue concerning spatiotemporal healthcare-socioeconomic relations, for which we derived data of county-level hospital beds number per capita, as well as data of related socioeconomic factors in northeast China during 2002–2011. Results showed that the STVC model surpassed all the other comparative regressions, in terms of both Bayesian model fitness and predictive ability. Globally, resident savings, financial institutions loans, GDP, and primary industry were identified as key socioeconomic conditions affecting healthcare resources in Northeast China. Temporally, with Time-Coefficients (TC) plots, we found that after 2011, GDP and primary industry would further help improve the overall healthcare level of northeast China. Spatially, with Space-Coefficients (SC) maps, we could directly identify the relative contribution of four socioeconomic covariates’ impacts on healthcare within each administrative county. Bayesian STVC model is an essential development and extension of the local regression family for exploring the spatiotemporal heterogeneous variables relationships, especially under Bayesian statistics, as well as GIScience and spatial statistics. Graphic abstract
Exploration of Plasma Lipids in Mild Cognitive Impairment due to Alzheimer's Disease.

BACKGROUND Lipids have important structural roles in cell membranes and changes to these membrane lipids may influence β- and γ-secretase activities and thus contribute to Alzheimer's disease (AD) pathology. OBJECTIVE To explore baseline plasma lipid profiling in participants with mild cognitive impairment (MCI) with and without AD pathology. METHODS We analyzed 261 plasma lipid profiles using reversed phase chromatography mass spectrometry in cerebrospinal fluid amyloid positive (Aβ+) or negative (Aβ-) participants with MCI as compared to controls. Additionally, we analyzed the potential associations of plasma lipid profiles with performance on neuropsychological tests at baseline and after two years. RESULTS Sphingomyelin (SM) concentrations, particularly, SM(d43:2), were lower in MCI Aβ+ individuals compared to controls. Further, SM(d43:2) was also nominally reduced in MCI Aβ+ individuals compared to MCI Aβ-. No plasma lipids were associated with performance on neuropsychological tests at baseline or between the two time points after correction for multiple testing. CONCLUSION Reduced plasma concentrations of SM were associated with AD.
Tumor-Infiltrating Lymphocytes in Biopsy Specimens Obtained 7 Days after Starting Chemoradiotherapy for Rectal Cancer Are Predictors of the Response to Chemoradiotherapy

Background: Neoadjuvant chemoradiotherapy (nCRT) followed by total mesorectal excision surgery is a standard treatment for locally advanced rectal cancer (LARC). Tumor-infiltrating lymphocytes (TILs) have been reported to be associated with tumor response; however, this remains to be established. We previously reported that histological changes on biopsy specimens obtained 7 days after starting nCRT are strong predictors of response to nCRT. Methods: The subjects were 208 patients with LARC who received nCRT. TILs on hematoxylin-eosin staining together with immunohistochemical staining of lymphocyte surface markers including CD3, CD4, CD8, and FoxP3 were performed both on the biopsy specimens before and 7 days after starting nCRT. Results: The proportions of patients with high densities of CD3+, CD4+, CD8+, and FoxP3+ cells 7 days after starting CRT were significantly lower than the respective values before starting nCRT (p < 0.0001, p < 0.0001, p = 0.0023, and p = 0.0046). In biopsy specimens obtained before treatment, high-density CD4+ cells and FOXP3+ cells were significantly associated with tumor shrinkage rate. High-density FOXP3+ cells were significantly associated with marked tumor regression. In biopsy specimens obtained 7 days after starting treatment, high-density CD4+ cells were significantly associated with marked tumor regression, tumor regression grade 1, and tumor shrinkage rate. High-density FoxP3+ cells were significantly associated with marked tumor regression and tumor shrinkage rate. Conclusions: In patients who received nCRT for LARC, the evaluations of immunohistochemical staining for CD4+ and FOXP3+ TILs were more intimately related to histological response to CRT and tumor shrinkage rates in biopsy specimens obtained 7 days after starting treatment than in biopsy specimens obtained before CRT.
Adverse events after pleurodesis in patients with malignant pleural effusion

Background Malignant pleural effusion (MPE) is an important sign of advanced disease in metastatic cancer. Pleurodesis is one option to treat recurrent MPE. The Inflammatory response after pleurodesis may lead to important adverse events (AE) in a set of very ill patients. Methods Retrospective analysis of patients submitted to pleurodesis (2009–2013). Clinical and laboratory data were collected. We compare the values in the day of pleurodesis, 2nd, 5th and 10th days after. Results One hundred fourteen patients were undergone to pleurodesis with silver nitrate (46%), iodine (52%) and talc (2%). Female was the most frequent (86%) and the breast cancer was the most common primary site. The most frequent adverse event was low hemoglobin account (37), followed by pain (31). 68% of patients presented AEs and 28% had at least one AE with grade 3 or higher. The most altered was CRP that peaked in the 5th day after pleurodesis. Changes in CRP curve were less severe with the use of iodine when compared with the other two agents. Conclusions Pleurodesis leads to important systemic inflammatory response detected by different serum markers. The occurrence of adverse events in this set of patients was great number of events with being marked as grade 3 or higher.
Atypical response patterns in metastatic melanoma and renal cell carcinoma patients treated with nivolumab: A single center experience

Introduction The response patterns of immune checkpoint inhibitors (ICIs) have been recognized to differ from those seen in standard cytotoxic and targeted therapy. Pseudoprogression and hyperprogression are new clinical phenomena specific to the field of immuno-oncology. In this study, we aimed to assess the frequency of hyperprogression and pseudoprogression in metastatic RCC and melanoma patients treated in our institution with the programmed cell death protein–1 inhibitor nivolumab. Methods The medical records of all metastatic melanoma and renal cell carcinoma patients that were treated with nivolumab (n = 54) in Bakirkoy Dr. Sadi Konuk Training and Research Hospital (Istanbul-Turkey), Medical Oncology Clinic between June 2017 and December 2019 were retrospectively analyzed. Results Hyperprogression and pseudoprogression rates were 12% and 9%, respectively and that is consistent with published data. Discussion Pseudoprogression and hyperprogression are new radiologic response patterns with immunotherapy agents. It is critical to be aware of these two phenomena in order to make the right decisions for patients.
Strategies for enhancing long-term carbon sequestration in mixed-species, naturally regenerated Northern temperate forests

Abstract We compared long-term C sequestration in the pools of aboveground portions of live trees, dead wood, and harvested wood products among highly contrasting forest management scenarios on a rotation (30-100 years) and 100-year basis. Average annual net change in C (AAC) and the cumulative sum of net changes in C were calculated using 65 years of data from permanent plots representing contrasting approaches to managing mixed-species stands dominated by shade-tolerant coniferous species on the Penobscot Experimental Forest in Maine, USA. Simulations of tree growth and mortality were used to estimate C pools to 100 years. On a rotation basis and for all pools combined, scenarios with selection cutting had greater AAC than those with shelterwood cutting followed by thinning or with diameter-limit cutting (p < 0.05). For combined pools, the cumulative sum of net changes in C for the unmanaged, selection, and guiding diameter-limit stands was positive for most of the study period. Our results suggest that strategies that maintain overstory stocking levels necessary to regenerate desired species and promote the development of sawlog-sized trees can enhance long-term C sequestration in mixed-species, naturally regenerated northern temperate forests.
Intention to be screened for Alzheimer’s disease in nondemented older adults: Integrated behavioral model and self-efficacy as mediation effect

ABSTRACT The study explored factors associated with intention to be screened for Alzheimer’s disease (AD). The study also examined whether self-efficacy mediates the relationship between knowledge about screening and the intention to be screened for AD. A population-based, random-digit dialing survey was performed and 1,043 responses were collected from a sample of nondemented persons (50 years or older) living in urban, suburban and rural areas in a Midwestern state. The findings showed that participants who were younger and who had higher levels of (a) perceived benefits and barriers, (b) social support and (c) self-efficacy reported higher levels of intention to be screened for AD. Older adults with positive life orientation reported greater intention to be screened for AD, whereas depressed participants were more likely to report a plan to be screened for AD. Self-efficacy mediated the relationship between knowledge about screening and intention to be screened. Older adults were more likely to report intention to be screened when they had positive attitudes about the screen and believed that they could receive the screen. The intention to be screened for AD could serve public awareness by defining effective ways to assist older adults to seek a cognitive screen.
Effective hemostasis in children with Von Willebrand factor defects undergoing adenotonsillar procedures

Abstract Introduction Children with low von Willebrand factor (VWF) activity or type 1 von Willebrand disease (VWD) have increased risk of bleeding after adenotonsillar procedures and the optimal perioperative management to minimize bleeding is unknown. Aim To report the effectiveness and safety of an institutional protocol in minimizing postoperative bleeding in children with type 1 VWD or low VWF activity. Methods We conducted a retrospective chart review in children with type 1 VWD or low VWF activity treated via an institutional protocol that utilizes repeated doses of Desmopressin acetate (DDAVP, 1-deamino 8-D arginine- vasopressin) or VWF concentrate, brief hospitalization for observation and extended use of oral epsilon aminocaproic acid (EACA). Results From 2010 to 2017, 13 children underwent an adenotonsillar procedure and were treated with this protocol. Although 7.6% had minor immediate bleeding and 23% had minor delayed bleeding, no patients experienced major bleeding or required transfusion, additional surgery or other measures not specified by the protocol. Mild hyponatremia was observed in 80% of patients who received DDAVP. Conclusion Our institutional protocol specifying repeated dosing of DDAVP or VWF concentrate to sustain elevated VWF levels during periods of highest bleeding risk and extended use of EACA is effective at preventing major bleeding episodes after adenotonsillar procedures. However, this analysis raised safety concerns that prompted changes in the institutional protocol and highlight the need for further prospective studies to determine the optimal strategy for safely reducing bleeding complications in these patients.
Ocular manifestation in progeria: A case report.

INTRODUCTION Progeria also known as Hutchinson Gilford Progeria Syndrome (HGPS) (MIM176670) is a very uncommon fatal genetic untimely aging syndrome. It is characterized by retarded physical development, accelerated degeneration of the skin, cardiovascular and musculoskeletal abnormalities. Other features include prominent eyes, thin nose, small chin and thin lips. Eyebrow hair loss, madarosis and lagopththalmos are the common ocular manifestations. CASE We report a case of five year old boy with complaints of discomfort in bright light and a whitish appearance in his right eye for two months. He was accompanied by the parents. They complained of loss of eyelashes and eyebrows. In the developmental history he was normal at birth till the age of one year then they noticed gradual hair fall, delayed growth, wrinkling of skin, increase in size of head and thinning of limbs. CONCLUSION This is the first case report from Nepal with the ocular presentation of progeria indicating the role of ocular senescence in patients with Hutchinson Progeria Gilford Syndrome.
Maternal intake of caffeinated products and birth defects: a systematic review and meta-analysis of observational studies

Abstract Caffeinated products are frequently consumed by women of childbearing age worldwide. It still unclear that whether maternal intake of caffeine associated with an increased risk of birth defects. We searched the databases of PubMed, Embase, the Cochrane Library, and Web of Science for eligible studies through July 2020. All studies examining the association between maternal consumption of caffeine or caffeinated products and birth defects were included. Twenty-nine studies were included in this meta-analysis. Among all the birth defects, maternal caffeine consumption was associated with a higher risk of cardiovascular defects, [odds ratio (OR) 1.17; 95% confidence interval (CI), 1.07–1.28], craniofacial defects (OR 1.09; 95% CI, 1.02–1.17), alimentary tract defects (OR 1.35; 95% CI, 1.16–1.56), and abdominal-wall defects and hernia (OR 1.13; 95% CI, 1.03–1.25). No association was found between maternal caffeine intake and musculoskeletal system defects, genitourinary system defects, nervous system defects, or chromosomal abnormalities. Meanwhile, all three of the caffeine consumption categories (low, moderate, and high) were associated with a higher risk of cardiovascular defects and alimentary tract defects.
Systematic Analysis of Escherichia coli Isolates from Sheep and Cattle Suggests Adaption to the Rumen Niche

As an important intestinal microorganism, E. coli is present in the intestinal tract of animals and in many other environments. However, it normally does not produce and secret cellulases due to its complex bilayer membrane structure and poor secretory apparatus. Here, we proved that E. coli is widely present in the rumen of sheep and cattle. Systematic analysis of the isolates indicated that they have adapted to the rumen niche, with phenotypes that include secretion of cellulase and fermentative accumulation of succinate and H2. The finding that overexpression of small heat shock protein genes ibpA and ibpB could facilitate cellulase BcsZ secretion, which provides a possible insight into the protein secretion mechanism of rumen-colonizing E. coli. ABSTRACT The commonly used laboratory bacterium Escherichia coli normally does not produce and secrete cellulases due to its complex bilayer membrane structure and poor secretory apparatus. In our previous study, the cellulolytic E. coli strain ZH-4 with extracellular cellulase activity was found in the bovine rumen. In this study, we demonstrate that the secretion of cellulase is a common feature of E. coli isolates from the rumen of animals such as sheep and cattle. Physiological phenotype characterization of these E. coli isolates, together with genome, transcriptome, and comparative genomics analysis, suggests their adaption to the rumen niche. The higher growth rate of the isolated strains under aerobic conditions meets the competitive requirements of the strains in rumen microecosystem, while anaerobic accumulation of reduced H2 and succinate is hypothesized to be the results of adaptation to the rumen environment. Cellulase secretion increased significantly when the molecular chaperone genes ibpA and ibpB were overexpressed. This was also revealed by the transcriptomic data. A possible mechanism for cellulase secretion by E. coli isolates was proposed based on the transcriptomic data and molecular experiments. IMPORTANCE As an important intestinal microorganism, E. coli is present in the intestinal tract of animals and in many other environments. However, it normally does not produce and secret cellulases due to its complex bilayer membrane structure and poor secretory apparatus. Here, we proved that E. coli is widely present in the rumen of sheep and cattle. Systematic analysis of the isolates indicated that they have adapted to the rumen niche, with phenotypes that include secretion of cellulase and fermentative accumulation of succinate and H2. The finding that overexpression of small heat shock protein genes ibpA and ibpB could facilitate cellulase BcsZ secretion, which provides a possible insight into the protein secretion mechanism of rumen-colonizing E. coli.
Association between consumption frequency of honey and non-alcoholic fatty liver disease: results from a cross-sectional analysis based on the Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIH) Cohort Study

Abstract Non-alcoholic fatty liver disease (NAFLD) is the hepatic manifestation of the metabolic syndrome. Recent evidence has suggested the protective effects of honey consumption against the metabolic syndrome, but the association between honey intake and NAFLD is still unclear. We investigated how the consumption frequency of honey was associated with NAFLD in the general population. This was a cross-sectional study of 21 979 adults aged 20–90 years. NAFLD was diagnosed based on the ultrasound-diagnosed fatty liver without significant alcohol intake and other liver diseases. Diet information, including consumption frequency of honey, was assessed by a validated 100-item FFQ. OR with 95 % CI were calculated by the binary logistic regression model, adjusting for confounding factors identified by the directed acyclic graph. Overall, 6513 adults (29·6 %) had NAFLD. Compared with participants consuming ≤1 time/week of honey, the multivariable OR of NAFLD were 0·86 (95 % CI 0·77, 0·97) for 2–6 times/week and 1·10 (95 % CI 0·95, 1·27) for ≥1 times/d (Pfor trend = 0·90). The results were generally similar in subgroups of BMI at a cut-point of 24·0 kg/m2 (Pfor interaction = 0·10). In this large-scale study, consuming honey 2–6 times/week was inversely associated with NAFLD, whereas consuming honey ≥1 times/d had no association with NAFLD. These results need replication in other large-scale prospective studies.
Factors influencing mixing and mass transfer in the small intestine : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Digestive Biomechanics (Physical Process of Digestion) at Massey University, Turitea, New Zealand

iii Table of contents . v List of Figures . xvii List of Tables. xxv List of Videos Referenced Throughout this Thesis. xxvi Preface . xxvii Acknowledgements . xxix Glossary . xxxii Chapter One Introduction . 1 Chapter Two Literature review. 5 2.1. Foreword . 6 2.2. Small intestinal motility . 7 Migrating motor complex (MMC) . 8 2.2.1. Peristalsis . 9 2.2.2. 2.2.2.1. Promotion of mass transfer . 11 Segmentation . 16 2.2. 3. 2.2. 3.1. Promotion of mass transfer . 19 Pendular activity. 20 2.2. 4. 2.2. 4.1. Promotion of mass transfer . 21
RCC2 Promotes Esophageal Cancer Growth by Regulating Activity and Expression of the Sox2 Transcription Factor

Regulator of chromosome condensation 2 (RCC2) is a protein located in the centrosome, which ensures that cell division proceeds properly. Previous reports show that RCC2 is overexpressed in some cancers and could play a key role in tumor development, but the mechanisms concerning how this occurs are not understood. Furthermore, no evidence exists regarding its role in esophageal cancer. We studied the relevance of RCC2 in esophageal cancer growth and its regulation on Sox2, an important transcription factor promoting esophageal cancer. RCC2 was overexpressed in esophageal tumors compared with normal tissue, and this overexpression was associated with tumorigenicity by increasing cell proliferation, anchorage-independent growth, and migration. These oncogenic effects were accompanied by overexpression of Sox2. RCC2 upregulated and stabilized Sox2 expression and its target genes by inhibiting ubiquitination-mediated proteasome degradation. Likewise, RCC2 increased the transcriptional activity and promoter binding of Sox2. In vivo studies indicated that RCC2 and Sox2 were overexpressed in esophageal tumors compared with normal tissue, and this upregulation occurs in the esophageal basal cell layer for both proteins. In conditional knockout mice, RCC2 deletion decreased the tumor nodule formation and progression in the esophagus compared with wild-type mice. Proliferating cell nuclear antigen expression, a cell proliferation marker, was also downregulated in RCC2 knockout mice. Overall, our data show for the first time that RCC2 is an important protein for the stabilization and transcriptional activation of Sox2 and further promotion of malignancy in esophageal cancer. Implications: This study shows that RCC2 controls Sox2 expression and transcriptional activity to mediate esophageal cancer formation.
Resilience Protective Factors Checklist (RPFC): Buffering Childhood Adversity and Promoting Positive Outcomes

While research tends to focus on understanding risk factors associated with adverse childhood and adolescent experiences, there is growing empirical support within the field of human services to also focus on strengths and protective factors that bolster resilience in life. This study investigated the psychometrics of the Resilience Protective Factors Checklist (RPFC), which is a questionnaire that assists in the identification of protective factors empirically linked to resilience and positive outcomes. In addition, associations between protective factors, childhood adversity, and quality of life outcomes were examined. Participants were undergraduate college students (n = 1,256). The results revealed good psychometric properties for the RPFC and the factor analysis supported the resilience structural model of three interrelated areas of protective factors - Individual, Family, and Community influences. All three areas of protection were positively correlated with all four domains of positive life outcomes (physical health, psychological health, social relationships, and a healthy environment) and negatively correlated with adverse childhood experiences. RPFC’s individual protective factors positively predicted physical health and psychological health outcomes, while the community protective factors positively predicted environmental health outcomes. In addition, the RPFC’s family protective factors moderated the path between adverse childhood experiences and social relationships. That is, for individuals who have experienced more adverse childhood experiences, those with higher levels of RPFC family protective factors had positive social relationship outcomes, while those with lower levels of family protective factors had negative social relationship outcomes. These findings lend support for the utilization of assessment measures for identifying and promoting protective factors that can buffer life adversity and heighten resilient positive outcomes.