Miracle-dz/UniFAR-FTUs huggingface dataset:
A Long-Term Trend Study of Tuberculosis Incidence in China, India and United States 1992–2017: A Joinpoint and Age–Period–Cohort Analysis

Tuberculosis (TB) is one of the major infectious diseases with the largest number of morbidity and mortality. Based on the comparison of high and low burden countries of tuberculosis in China, India and the United States, the influence of age-period-cohort on the incidence of tuberculosis in three countries from 1992 to 2017 was studied based on the Global burden of Disease Study 2017. We studied the trends using Joinpoint regression in the age-standardized incidence rate (ASIR). The regression model showed a significant decreasing behavior in China, India and the United States between 1992 and 2017. Here, we analyzed the tuberculosis incidence trends in China, India, as well as the United States and distinguished age, period and cohort effects by using age-period-cohort (APC) model. We found that the relative risks (RRs) of tuberculosis in China and India have similar trends, but the United States was found different. The period effect showed that the incidence of the three countries as a whole declines with time. The incidence of tuberculosis had increased in most age group. The older the age, the higher the risk of TB incidence. The net age effect in China and India showed a negative trend, while the cohort effect decreased from the earlier birth cohort to the recent birth cohort. Aging may lead to a continuous increase in the incidence of tuberculosis. It is related to the aging of the population and the relative decline of the immune function in the elderly. This should be timely population intervention or vaccine measures, especially for the elderly. The net cohort effect in the United States showed an unfavorable trend, mainly due to rising smoking rates and the emergence of an economic crisis. Reducing tobacco consumption can effectively reduce the incidence.
Fluorescent Carbon Quantum Dots—Synthesis, Functionalization and Sensing Application in Food Analysis

Carbon quantum dots (CQDs) with stable physicochemical properties are one of the emerging carbon nanomaterials that have been studied in recent years. In addition to the excellent optical properties such as photoluminescence, photobleaching resistance and light stability, this material also has favorable advantages of good biocompatibility and easy functionalization, which make it an ideal raw material for constructing sensing equipment. In addition, CQDs can combined with other kinds of materials to form the nanostructured composites with unique properties, which provides new insights and ideas for the research of many fields. In the field of food analysis, emerging CQDs have been deeply studied in food composition analysis, detection and monitoring trace harmful substances and made remarkable research progress. This article introduces and compares the various methods for CQDs preparation and reviews its related sensing applications as a new material in food components analysis and food safety inspection in recent years. It is expected to provide a significant guidance for the further study of CQDs in the field of food analysis and detection.
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

Abstract Major histocompatibility complex (MHC) molecules are expressed on the cell surface, where they present peptides to T cells, which gives them a key role in the development of T-cell immune responses. MHC molecules come in two main variants: MHC Class I (MHC-I) and MHC Class II (MHC-II). MHC-I predominantly present peptides derived from intracellular proteins, whereas MHC-II predominantly presents peptides from extracellular proteins. In both cases, the binding between MHC and antigenic peptides is the most selective step in the antigen presentation pathway. Therefore, the prediction of peptide binding to MHC is a powerful utility to predict the possible specificity of a T-cell immune response. Commonly MHC binding prediction tools are trained on binding affinity or mass spectrometry-eluted ligands. Recent studies have however demonstrated how the integration of both data types can boost predictive performances. Inspired by this, we here present NetMHCpan-4.1 and NetMHCIIpan-4.0, two web servers created to predict binding between peptides and MHC-I and MHC-II, respectively. Both methods exploit tailored machine learning strategies to integrate different training data types, resulting in state-of-the-art performance and outperforming their competitors. The servers are available at http://www.cbs. dtu.dk/services/NetMHCpan-4.1/ and http://www.cbs. dtu.dk/services/NetMHCIIpan-4.0/.
Usefulness of Kidney Donor Profile Index (KDPI) to predict graft survival in a South Brazilian Cohort

Abstract Introduction: Kidney Donor Profile Index (KDPI) has been incorporated in the United States to improve the kidney transplant allocation system. Objectives: To evaluate deceased kidney donors’ profile using KDPI and compare to the previous United Network for Organ Sharing (UNOS) definition of expanded criteria donors (ECD) and assess the KDPI applicability to predict five-year graft survival and renal function in our sample. Methods: Retrospective cohort of 589 kidney transplants from deceased donors performed from January 2009 to May 2013 with follow-up until May 2018. Results: In 589 kidney transplants, 36.6% of donors were classified as ECD and 28.8% had KDPI ≥ 85%. Mean KDPI was 63.1 (95%CI: 60.8-65.3). There was an overlap of standard and ECD in KDPI between 60 and 95 and a significantly lower death-censored graft survival in KDPI ≥ 85% (78.6%); KDPI 0-20: 89.8%, KDPI 21-59: 91.6%, and KDPI 60-84: 83.0%; p = 0.006. The AUC-ROC was 0.577 (95%CI: 0.514-0.641; p = 0.027). Renal function at 5 years was significantly lower according to the incremental KDPI (p < 0.002). KDPI (HR 1.011; 95%CI 1.001-1.020; p = 0.008), donor-specific antibodies (HR 2.77; 95%CI 1.69-4.54; p < 0.001), acute rejection episode (HR 1.73; 95%CI 1.04-2.86; p = 0.034) were independent and significant risk factors for death-censored graft loss at 5 years. Conclusion: In our study, 36.6% were classified as ECD and 28.8% had KDPI ≥ 85%. KDPI score showed a moderate power to predict graft survival at 5 years. Renal function was significantly lower in patients with higher KDPI.
Economics of Five Wheat Production Systems with No-Till and Conventional Tillage

Conventional tillage (CT) continues to be used on the vast majority of land seeded to monoculture winter wheat (Triticum aestivum L.) in the Southern Plains of the United States. In the region, wheat can be grown for either grain-only, forage-only, or for both fall-winter forage + grain (dual-purpose). This study was conducted to determine the net returns of five alternative wheat production systems, for both CT and no-till (NT). The five production systems included one for forage-only, two for dual-purpose (fall-winter grazing + grain) with different planting dates, one grain-only, and one forage-only double cropped with foxtail millet [Setaria italica (L.) Beauv. ]. The field research was conducted on three farm fields for 3 yr. Average wheat grain yields were greater with CT, whereas average fall wheat forage yields were significantly greater on the NT plots. Wheat hay and millet hay yields were not significantly different across tillage systems. Economic analysis was conducted for both a machinery complement sized for a 260-ha farm and a machinery complement sized for a 1036-ha farm. For both farm sizes and both tillage systems, the early-September-planted dual-purpose system (ESD) produced the greatest net returns. For the 260-ha farm, CT produced greater net returns than NT for each of the five production systems. Conventional tillage also produced greater economic returns for the three systems that included grain harvest for the 1036-ha farm. However, for the larger farm size, NT generated greater net returns for both total forage systems.
A guiding torch at the poles: the multiple roles of spindle microtubule-organizing centers during cell division

ABSTRACT The spindle constitutes the cellular machinery that enables the segregation of the chromosomes during eukaryotic cell division. The microtubules that form this fascinating and complex genome distribution system emanate from specialized structures located at both its poles and known as microtubule-organizing centers (MTOCs). Beyond their structural function, the spindle MTOCs play fundamental roles in cell cycle control, the activation and functionality of the mitotic checkpoints and during cellular aging. This review highlights the pivotal importance of spindle-associated MTOCs in multiple cellular processes and their central role as key regulatory hubs where diverse intracellular signals are integrated and coordinated to ensure the successful completion of cell division and the maintenance of the replicative lifespan.
Exploiting the Prevalence of Homologous Recombination Deficiencies in High-Grade Serous Ovarian Cancer

High-grade serous ovarian cancer (HGSOC) remains the most lethal gynecologic cancer in the United States. Genomic analysis revealed roughly half of HGSOC display homologous repair deficiencies. An improved understanding of the genomic and somatic mutations that influence DNA repair led to the development of poly(ADP-ribose) polymerase inhibitors for the treatment of ovarian cancer. In this review, we explore the preclinical and clinical studies that led to the development of FDA approved drugs that take advantage of the synthetic lethality concept, the implementation of the early phase trials, the development of companion diagnostics and proposed mechanisms of resistance.
Panax quinquefolium L. Ginsenosides from Hairy Root Cultures and Their Clones Exert Cytotoxic, Genotoxic and Pro-Apoptotic Activity towards Human Colon Adenocarcinoma Cell Line Caco-2

American ginseng, Panax quinquefolium (L.), is traditionally used in folk medicine. It exhibits a range of anti-inflammatory, hepatoprotective, anti-diabetic, anti-obesity, anti-hyperlipidemic and anti-carcinogenic effects. Its main components are ginsenosides, also known as panaxosides or triterpene saponins. In order to obtain high yields of ginsenosides, different methods of controlled production are involved, i.e., with hairy root cultures. However, they are still employed under in vitro conditions. Our studies revealed that hairy root cultures subjected to an elicitation process can be considered as a potent source of ginsenosides. The present study examines the biological activity of ginseng hairy root cultures against the Caco-2 human adenocarcinoma cell line. Among our six different clones of P. quinquefolium hairy roots, extracts B and Be (treated with elicitor) were the strongest inhibitors of the cellular metabolic activity. While all extracts induced DNA damage, B and Be also generated reactive oxygen species (ROS) in a concentration-dependent manner, which was correlated with the depletion of the mitochondrial membrane potential and induction of apoptosis. These findings indicate that further research concerning P. quinquefolium hairy root cultures should focus on the activity of rare ginsenosides and other biologically active compound profiles (i.e., phenolic compounds).
Regorafenib and Nivolumab or Pembrolizumab Combination and Circulating Tumor DNA Response Assessment in Refractory Microsatellite Stable Colorectal Cancer

Abstract Background Metastatic colorectal cancers (MCRCs) with microsatellite stability (MSS) are resistant to immunotherapy with programmed cell death protein 1 (PD‐1) and programmed death‐ligand 1 inhibitors. However, the addition of regorafenib to nivolumab was recently associated with a high response rate and a protracted progression‐free survival in a small cohort of MSS Japanese patients with metastatic colorectal cancer. Materials and Methods We evaluated the outcome of patients with MSS metastatic colorectal cancer who were treated on a compassionate basis with PD‐1 inhibitors in combination with regorafenib in a single U.S. center. Results A total of 18 patients were treated with a combination of regorafenib and PD‐1 inhibitors. No treatment‐related grade 3 or above toxicities were noted. Thirteen patients (69%) had progressive disease, and five patients (31%) experienced stable disease as best response. Four out of five stable diseases occurred in patients without liver metastases, whereas only 1 of 14 patients with history of liver metastases had a short disease stabilization. A rise in circulating tumor DNA (ctDNA) at the 4‐week time pointuniversally predicted tumor progression at 2 months, whereas a decline was associated with radiographic disease stabilization. Conclusions Regorafenib and nivolumab combination was associated with modest clinical activity in patients with MSS chemotherapy‐resistant metastatic colorectal cancer. Selection for patients without history of liver metastases may identify a cohort of patients with MSS colorectal cancer with a higher likelihood of benefit from this combination. ctDNA may represent a powerful tool for predicting early therapeutic efficacy of immunotherapy in the MSS colorectal cancer population. Implications for Practice This study showed that the combination of regorafenib and nivolumab was associated with a modest clinical activity in patients with advanced microsatellite stability (MSS) metastatic colorectal cancer. This combination should be avoided in clinical practice, especially in patients with MSS colorectal cancer with liver metastases. Further investigation of regorafenib plus PD‐1 inhibitors should be considered in MSS colorectal cancer without liver metastases.
Effect of high-salt diet on blood pressure and body fluid composition in patients with type 1 diabetes: randomized controlled intervention trial

Introduction Patients with type 1 diabetes are susceptible to hypertension, possibly resulting from increased salt sensitivity and accompanied changes in body fluid composition. We examined the effect of a high-salt diet (HSD) in type 1 diabetes on hemodynamics, including blood pressure (BP) and body fluid composition. Research design and methods We studied eight male patients with type 1 diabetes and 12 matched healthy controls with normal BP, body mass index, and renal function. All subjects adhered to a low-salt diet and HSD for eight days in randomized order. On day 8 of each diet, extracellular fluid volume (ECFV) and plasma volume were calculated with the use of iohexol and 125I-albumin distribution. Hemodynamic measurements included BP, cardiac output (CO), and systemic vascular resistance. Results After HSD, patients with type 1 diabetes showed a BP increase (mean arterial pressure: 85 (5) mm Hg vs 80 (3) mm Hg; p<0.05), while BP in controls did not rise (78 (5) mm Hg vs 78 (5) mm Hg). Plasma volume increased after HSD in patients with type 1 diabetes (p<0.05) and not in controls (p=0.23). There was no significant difference in ECFV between diets, while HSD significantly increased CO, heart rate (HR) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) in type 1 diabetes but not in controls. There were no significant differences in systemic vascular resistance, although there was a trend towards an HSD-induced decrease in controls (p=0.09). Conclusions In the present study, patients with type 1 diabetes show a salt-sensitive BP rise to HSD, which is accompanied by significant increases in plasma volume, CO, HR, and NT-proBNP. Underlying mechanisms for these responses need further research in order to unravel the increased susceptibility to hypertension and cardiovascular disease in diabetes. Trial registration numbers NTR4095 and NTR4788.
Functional Traits, Morphology, and Herbage Production of Vernalised and Non-Vernalised Chicory cv. Choice (Cichorium intybus L.) in Response to Defoliation Frequency and Height

Chicory (Cichorium intybus L.) used in pastoral systems has the attributes required of a forage species to reduce animal urinary nitrogen loading to soil, increase milk production, and enhance milk fatty acid profile to improve pastoral farm systems for matching increasing global demand for dairy products and environmental standards of livestock systems. Greater adoption of chicory requires confidence in management decisions that can control risks to farm production, namely bolting after vernalisation or a decline in persistence of chicory swards, which have slowed its adoption in pastoral systems. We, therefore, measured functional traits, morphology and herbage production of chicory under irrigated field conditions before and after vernalisation in Canterbury, New Zealand. The experimental site was laid out in a complete randomized block design with four replications where two regrowth intervals and two defoliation heights were applied. Regrowth interval had a stronger influence over functional traits and herbage production than defoliation height, with more pronounced effects after vernalisation. Plants managed under shorter regrowth intervals had narrower roots with lower concentration of sugars than plants under longer intervals, which might compromise their longevity. In addition, plants managed under shorter intervals remained mostly vegetative with heavier and longer leaves, though with reduced photosynthetic capacity than those managed under longer intervals. The thermal time to initiate stem elongation in plants managed under longer intervals was ~274 growing degree-days, with a mean stem elongation rate increasing linearly at 1.4 ± 0.08 mm/growing degree-days. The key outcomes of this research quantify the growing degree-days to initiate stem elongation post vernalisation, which provides management directive for timing of defoliation of chicory in order to maintain feed quality for grazing livestock. Alternating frequent and infrequent defoliation regimes might be used to optimise vegetative growth, root reserves, and pasture persistence.
Applications of Artificial Intelligence to Prostate Multiparametric MRI (mpMRI): Current and Emerging Trends

Prostate carcinoma is one of the most prevalent cancers worldwide. Multiparametric magnetic resonance imaging (mpMRI) is a non-invasive tool that can improve prostate lesion detection, classification, and volume quantification. Machine learning (ML), a branch of artificial intelligence, can rapidly and accurately analyze mpMRI images. ML could provide better standardization and consistency in identifying prostate lesions and enhance prostate carcinoma management. This review summarizes ML applications to prostate mpMRI and focuses on prostate organ segmentation, lesion detection and segmentation, and lesion characterization. A literature search was conducted to find studies that have applied ML methods to prostate mpMRI. To date, prostate organ segmentation and volume approximation have been well executed using various ML techniques. Prostate lesion detection and segmentation are much more challenging tasks for ML and were attempted in several studies. They largely remain unsolved problems due to data scarcity and the limitations of current ML algorithms. By contrast, prostate lesion characterization has been successfully completed in several studies because of better data availability. Overall, ML is well situated to become a tool that enhances radiologists’ accuracy and speed.
Size‐dependent visual predation risk and the timing of vertical migration in zooplankton

Zooplankton commonly exhibit diel vertical migration (DVM), descending from food‐rich surface waters during the day. If DVM is a tradeoff between avoiding size‐selective visually hunting predators and maximizing energy gain, smaller bodied prey should enter surface waters earlier and leave later than larger, more visually conspicuous organisms. Conventional sampling technologies lack the temporal resolution to test this prediction. Here, we report on the first test of this prediction using a new submersible optical‐acoustic imaging system capable of resolving the timing of migration of the euphausiid crustacean Euphausia pacifica Hansen. Smaller bodied animals consistently ascended as much as 30 min earlier and descended up to 45 min later than adults. The timing of vertical migration reflects how the size‐dependent risk of attack by visual predators alters the tradeoff between feeding and predator avoidance, supporting the predator‐avoidance hypothesis for DVM.
The language of dying: Communication about end-of-life in residential aged care

Abstract This article explores implications of language used in communicating death and dying in residential aged care, which increasingly emphasizes a “family-centered” approach to end-of-life care. Based on focus groups with care professionals and families, our findings reveal a persistent clinical culture that resists frank discussions of dying, with many staff preferring to use euphemisms for dying. Our results emphasize the importance of end-of-life education for families, which families acknowledged was lacking. Cultural change in institutional control over disclosing dying is imperative in order to gain family trust and support in professional care and promote death literacy.
Tidal Mixing and Summer Plankton Distributions in Hecate Strait, British Columbia

Summer plankton distributions in Hecate Strait, northern British Columbia, were examined during 1979 and 1980 and compared with tidal mixing characteristics. Calculations of the Simpson–Hunter tidal stratification parameter (h∙U−3) indicate that most of Hecate Strait is potentially stratified in summer (in the absence of excessive storms), with a well-mixed region over the shallow shelf adjacent to the Queen Charlotte Islands. Vertical temperature profiles collected from a coastal oil tanker ship of opportunity confirmed the presence of mixed and stratified water masses as predicted. Near-surface concentrations of chlorophyll a, nutrients, diatoms, and copepods were lower in the mixed region (< 1 μg Chl. a∙L−1) than the statified region, but highest (5 μg Chl. a∙L−1) at the front between these mixing regimes. We believe that low phytoplankton biomass in western mixed waters is due to nutrient rather than light limitation, whereas possible advection of nutrients along the edge of the western shelf may supp.
Analysis of SCN9A Gene Variants for Acute and Chronic Postoperative Pain and Morphine Consumption After Total Hysterectomy.

BACKGROUND Single nucleotide polymorphisms (SNPs) of the voltage-gated sodium channel alpha subunit gene (SCN9A) have been associated with pain in various settings. The aim of this study was to investigate the association of the SNPs to evaluate the influence of common gene variants on chronic postoperative pain (CPSP) and other related pain variables in a cohort of patients who underwent a scheduled hysterectomy. METHODS DNA samples from a cohort of 1,075 patients who underwent a scheduled total hysterectomy in our hospital were genotyped for three common SCN9A SNPs using TaqMan assays. Multivariate logistic regression models were used to quantify the association between independent covariates such as pain threshold, pain endurance, pain scores, morphine use, and the presence of chronic pain. RESULTS Frequencies of the minor alleles were different between the different ethnic groups. There was a statistically significant association of rs16851799 with morphine consumption and self-reported postoperative pain for the 1,038 subjects genotyped, with the TT genotype reporting higher pain and using more morphine. For the subpopulation of 446 subjects with chronic pain data, there was a similar association with self-reported postoperative pain and tolerance of pressure pain. Univariate analysis also showed a statistically significant association of rs16851799 with CPSP, whereas multivariable analysis revealed a similar association of rs4387806 with this outcome. There were three haplotypes with different relative frequencies for the CPSP and non-CPSP groups. CONCLUSIONS Our results showed that SCN9A polymorphisms could play a role in acute pain perception and the susceptibility to chronic pain.