Miracle-dz/UniFAR-FTUs huggingface dataset:
Operating at the extreme: estimating the upper yield boundary of winter wheat production in commercial practice

Wheat farming provides 28.5% of global cereal production. After steady growth in average crop yield from 1950 to 1990, wheat yields have generally stagnated, which prompts the question of whether further improvements are possible. Statistical studies of agronomic parameters such as crop yield have so far exclusively focused on estimating parameters describing the whole of the data, rather than the highest yields specifically. These indicators include the mean or median yield of a crop, or finding the combinations of agronomic traits that are correlated with increasing average yields. In this paper, we take an alternative approach and consider high yields only. We carry out an extreme value analysis of winter wheat yield data collected in England and Wales between 2006 and 2015. This analysis suggests that, under current climate and growing conditions, there is indeed a finite upper bound for winter wheat yield, whose value we estimate to be 17.60 tonnes per hectare. We then refine the analysis for strata defined by either location or level of use of agricultural inputs. We find that there is no statistical evidence for variation of maximal yield depending on location, and neither is there statistical evidence that maximum yield levels are improved by high levels of crop protection and fertilizer use.
Serum Biomarkers for Inflammatory Bowel Disease

Background: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic, inflammatory disorder of the gastrointestinal tract. As the novel therapeutic goal and biologicals are widely recognized, accurate assessment of disease and prediction of therapeutic response have become a crucial challenge in clinical practice. Also, because of the continuously rising incidence, convenient and economical methods of diagnosis and clinical assessment are urgently needed. Recently, serum biomarkers have made a great progress and become a focus in IBD study because they are non-invasive, convenient, and relatively inexpensive than are markers in biopsy tissue, stool, breath, and other body fluids. Aims: To review the available data on serological biomarkers for IBD. Methods: We searched PubMed using predefined key words on relevant literatures of serum biomarkers regarding diagnosis, evaluation of therapeutic efficacy, surveillance of disease activity, and assessment of prognosis for IBD. Results: We reviewed serological biomarkers that are well-established and widely used (e.g., C-reactive protein), newly discovered biomarkers (e.g., cytokines, antibodies, and non-coding RNAs), and also recently advancements in serological biomarkers (e.g., metabolomics and proteomics) that are used in different aspects of IBD management. Conclusions: With such a wealth of researches, to date, there are still no ideal serum biomarkers for IBD. Serum profiling and non-coding RNAs are just starting to blossom but reveal great promise for future clinical practice. Combining different biomarkers can be valuable in improving performance of disease evaluation.
Live Vaccines Have Different NK Cells and Neutrophils Requirements for the Development of a Protective Immune Response Against Tuberculosis

It has been shown that neutrophils drive NK cells to activate DCs while NK cells regulate neutrophils survival. In response to mycobacteria, NK cells proliferate and produces IFN-γ, that appears to regulate the neutrophilic inflammatory responses to both M. tuberculosis infection and BCG vaccination. Although the role of neutrophils in the immune response to tuberculosis is a matter of debate, neutrophils were shown to be crucial to induce specific response against mc2-CMX vaccine. The objective of this study was to investigate the interplay between NK cells and neutrophils in regard to the development of a protective immune response against M. tuberculosis. Depletion of NK cells during vaccination did not alter the total number of neutrophils or DCs, but reduced the number of activated DCs, thus reducing the generation of Th1 specific immune responses and the protection conferred by mc2-CMX and BCG vaccines. However, only in mc2-CMX vaccination that neutrophil depletion interfered with the NK cell numbers and protection. In conclusion, it was shown that only when both NK and neutrophils were present, specific Th1 response and protection was achieved by mc2-CMX vaccine, while neutrophils although activated upon BCG vaccination were not necessary for the induced protection.
The effect of seed size and planting depth on the yield of seed potatoes grown from minitubers

Experiments were carried out in 1993 to 1995 inclusive to investigate the effect of tuber size and depth of planting of minitubers on the progeny seed numbers and yield. Four tuber sizes, 12 to 15 mm, 15 to 20 mm, 20 to 25 mm and 25 to 30 mm were used and they were planted at depths of 5.0 cm, 7.5 cm and 10.0 cm. Early ground cover was improved as the seed size used was increased while varying the depth of planting usually had little effect. Increasing seed size produced larger total progeny tuber numbers and greater numbers in the seed fraction while increasing the depth of planting reduced tuber numbers in the seed fraction in two years out of three. Progeny seed yields increased as the seed size was increased and increasing the planting depth to 10.0 cm tended to reduce yields in two years out of three. Even though progeny seed yields and tuber numbers in the seed fraction were increased by using larger seed sizes, the smallest seed size used (12 to 15 mm) was suitable and produced viable seed yields and tuber numbers. A planting depth of 5.0 cm was suitable but it was necessary to mould up the drills after emergence.
Marine Microbial Community Composition During the Upwelling Season in the Southern Benguela

The microbial communities of the southern Benguela upwelling region were sampled quarterly through 1 year, with sampling for prokaryotes taking place in May, September, November and February, spanning the 2015–2016 upwelling season. Picoeukaryote samples were taken in November and February only. Community dynamics were assessed at stations both inside and outside a typical upwelling site. 16S and 18S rRNA amplicon results, respectively, revealed differences in both bacterioplankton and picoeukaryote communities in both space and time (season). There was a significant difference between sites in picoeukaryote community structure and diversity during the upwelling season in February, but not in November. Prokaryote community structure showed significant changes by water type as well as by sampling time or site. The parasitic dinoflagellate, Syndiniales, dominated February samples, and diatoms (Mediophyceae) mostly occurred in November samples, with nitrate driving community structure. Prokaryote results revealed presence of Nitrosopumillus, an ammonium oxidizer, offshore in February. Nitrospina sp. , a nitrite oxidizer, was also present in September in hypoxic and deep water samples. This study reveals significant changes in community variability, leading to shifts within interspecies interactions in this region in response to upwelling events. This has far reaching implications with regard to biogeochemical cycling and ecosystem functioning at the microbial level.
Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant

Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes (“typical” and “high stem” form) identified early in our study. With distinct morphologies and distribution, the “high stem” form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.
Seasonal Movement Patterns of the Bigfin Reef Squid Sepioteuthis lessoniana Predicted Using Statolith δ18O Values

Sepioteuthis lessoniana is a widely distributed neritic squid in the Indo-Pacific Ocean. It is an important species in fisheries, but species management is difficult because of inadequate information regarding its life history. The daily growth and δ18O values from the core to the edge of statoliths of S. lessoniana collected in northern Taiwan were analyzed to predict the experienced temperature history along with ontogenetic stages. The probability of occurrence in a given area at each life stage in three seasonal groups was determined using salinity values, deduced and measured temperatures, and the known ecology of S. lessoniana. The results showed that ontogenetic variation in the statolith δ18O values in S. lessoniana reflected the seasonal temperature fluctuation observed in Taiwanese waters, which indicated the reliability of the prediction method. Complex and diverse distribution and movement patterns were observed in the three seasonal groups. The results also indicated the importance of the waters near the coast of northeastern Taiwan as a spawning ground. Based on a model prediction, the distribution of S. lessoniana is likely associated with water temperature and current. A potential migration route from the Penghu Islands to northeastern Taiwan suggests a high level of population connectivity in S. lessoniana in Taiwan. This study provides information on the spatial and vertical distribution of S. lessoniana at various ontogenetic stages, which is essential for resource management and conservation of this commercial species.
General Adaptation in Critical Illness: Glucocorticoid Receptor-alpha Master Regulator of Homeostatic Corrections

In critical illness, homeostatic corrections representing the culmination of hundreds of millions of years of evolution, are modulated by the activated glucocorticoid receptor alpha (GRα) and are associated with an enormous bioenergetic and metabolic cost. Appreciation of how homeostatic corrections work and how they evolved provides a conceptual framework to understand the complex pathobiology of critical illness. Emerging literature place the activated GRα at the center of all phases of disease development and resolution, including activation and re-enforcement of innate immunity, downregulation of pro-inflammatory transcription factors, and restoration of anatomy and function. By the time critically ill patients necessitate vital organ support for survival, they have reached near exhaustion or exhaustion of neuroendocrine homeostatic compensation, cell bio-energetic and adaptation functions, and reserves of vital micronutrients. We review how critical illness-related corticosteroid insufficiency, mitochondrial dysfunction/damage, and hypovitaminosis collectively interact to accelerate an anti-homeostatic active process of natural selection. Importantly, the allostatic overload imposed by these homeostatic corrections impacts negatively on both acute and long-term morbidity and mortality. Since the bioenergetic and metabolic reserves to support homeostatic corrections are time-limited, early interventions should be directed at increasing GRα and mitochondria number and function. Present understanding of the activated GC-GRα's role in immunomodulation and disease resolution should be taken into account when re-evaluating how to administer glucocorticoid treatment and co-interventions to improve cellular responsiveness. The activated GRα interdependence with functional mitochondria and three vitamin reserves (B1, C, and D) provides a rationale for co-interventions that include prolonged glucocorticoid treatment in association with rapid correction of hypovitaminosis.
Cross-Dataset Variability Problem in EEG Decoding With Deep Learning

Cross-subject variability problems hinder practical usages of Brain-Computer Interfaces. Recently, deep learning has been introduced into the BCI community due to its better generalization and feature representation abilities. However, most studies currently only have validated deep learning models for single datasets, and the generalization ability for other datasets still needs to be further verified. In this paper, we validated deep learning models for eight MI datasets and demonstrated that the cross-dataset variability problem weakened the generalization ability of models. To alleviate the impact of cross-dataset variability, we proposed an online pre-alignment strategy for aligning the EEG distributions of different subjects before training and inference processes. The results of this study show that deep learning models with online pre-alignment strategies could significantly improve the generalization ability across datasets without any additional calibration data.
Astrocytic Glutamate Transporter 1 (GLT1) Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice

Glutamatergic dysregulation is known to contribute to altered emotional regulation. Astrocytic glutamate transporter 1 (GLT1) is responsible for the majority of glutamate clearance from synapse. However, the role of astrocytic GLT1 in affective processes such as anxiety- and depression-like behavior is not fully understood. Here, we found that astrocytic GLT1 deficient mice entered more frequently, and spent more time in the open arms of elevated plus maze without difference in overall distance traveled in the open field, nor were there any metabolic changes observed in the metabolic chamber compared to wildtype mice. Moreover, mice lacking astrocytic GLT1 exhibited less immobile time and moved greater area in the tail suspension test. Similarly, in the forced swim test, they showed less immobile time and moved greater area. In addition, we found that astrocytic GLT1 deficiency reduced freezing responses in the fear contextual and cued tests. Taken together, our findings suggest that astrocytic GLT1 deficiency decreases anxiety and depression-like behaviors.
Multicenter Placebo-Controlled Randomized Study of Ethyl Pyruvate in Horses Following Surgical Treatment for ≥ 360° Large Colon Volvulus

Identifying therapies that mitigate ischemic colonic injury and improve mucosal healing and intestinal viability are crucial to improving survival in horses with ≥360° large colon volvulus (LCV). Ethyl pyruvate is the ethyl ester of pyruvate with diverse pharmacologic effects that limit ischemic injury and hasten intestinal mucosal repair in preclinical rodents, sheep and swine models. The objective of this study was to determine the effects of ethyl pyruvate on systemic indices of colon viability, expression of inflammatory genes in whole blood, morbidity and survival after surgical correction of LCV compared to controls. Horses received either 150 mg/kg ethyl pyruvate in 1 liter lactated Ringer's solution (LRS) or 1 liter LRS intravenously (IV) every 6 h for 24 h following surgical recovery for correction of LCV. Colic duration, perioperative heart rate (HR), packed cell volume (PCV), total solids (TS), blood L-lactate concentration, surgical time, intraoperative episodes of hypoxemia and hypotension, expression of inflammatory cytokine genes, fecal consistency and survival to hospital discharge were compared between ethyl pyruvate treated horses and controls. Twenty-two horses, 12 receiving ethyl pyruvate and 10 controls, were enrolled in the study. Ethyl pyruvate was safely administered to horses following surgical correction of LCV. No significant effects of ethyl pyruvate on post-operative variables, including survival, were found. Seven of 12 ethyl pyruvate treated horses and 5/10 controls survived to hospital discharge. Higher HR, PCV and blood L-lactate concentration at the time of hospital admission, P = 0.005, 0.01, 0.04, respectively, 24 h after surgery, P = 0.001, 0.03, 0.02, respectively, were associated with death. Heart rate, P = 0.005, 48 h after surgery was associated with death. Ethyl pyruvate was safely administered to horses following correction of LCV with no apparent adverse events but was not associated with improved post-operative outcomes including survival. A larger, randomized control trial is needed to fully evaluate the effectiveness of ethyl pyruvate. A major limitation of this investigation is the small sample size, making the study underpowered and creating a high possibility of type II error.
Methods for Accurate Assessment of Myofiber Maturity During Skeletal Muscle Regeneration

Adult skeletal muscle has a remarkable ability to regenerate. Regeneration of mature muscle fibers is dependent on muscle stem cells called satellite cells. Although they are normally in a quiescent state, satellite cells are rapidly activated after injury, and subsequently proliferate and differentiate to make new muscle fibers. Myogenesis is a highly orchestrated biological process and has been extensively studied, and therefore many parameters that can precisely evaluate regenerating events have been established. However, in some cases, it is necessary to evaluate the completion of regeneration rather than ongoing regeneration. In this study, we establish methods for assessing the myofiber maturation during muscle regeneration. By carefully comparing expression patterns of several muscle regeneration-related genes, we found that expression of Myozenin (Myoz1 and Myoz3), Troponin I (Tnni2), and Dystrophin (Dmd) is gradually increased as muscle regeneration proceeds. In contrast, commonly used regeneration markers such as Myh3 and Myh8 are transiently upregulated after muscle injury but their expression decreases as regeneration progresses. Intriguingly, upregulation of Myoz1, Myoz3 and Tnni2 cannot be achieved in cultured myotubes, indicating that these markers are excellent indicators to assess myofiber maturity. We also show that analyzing re-expression of Myoz1 and dystrophin in individual fiber during regeneration enables accurate assessment of myofiber maturity at the single-myofiber level. Together, our study provides valuable methods that are useful in evaluating muscle regeneration and the efficacy of therapeutic strategies for muscle diseases.
Loess-Palaeosol Sequences in the Kashmir Valley, NW Himalayas: A Review

Loess deposits and intercalated palaeosols are widespread in the Quaternary record, and these have been extensively used to gain insights into continental paleoclimatic and paleo-environmental conditions and changes. Especially over Eurasia, loess geoarchives play an important role for our understanding of past changes. Loess covers almost 500 km2 of the Kashmir Valley in north-western India, it occurs dominantly in plateau positions, but also on terraces and sometimes forms slope deposits with thicknesses ranging from several to more than 20 m. For the time being, however, the timing of the initiation of the loess accumulation, the provenance, the grain size composition and also the paleo-environment have not been studied systematically and yet only little quantitative data is available. Yet it is clear that deposition rates are at least comparable to European loess, and that the presence of multiple palaeosols intercalated in the loess can provide valuable information on the history of the region. The limited available data hinders regional and continental correlation, and tapping its value as archive of past environmental changes in this sensitive region with influence from Westerlies and the Indian Monsoon. However, several characteristic palaeosol patterns can be traced throughout the Kashmir valley, which provide stratigraphic information. Several studies investigate physical and chemical properties of the loess-paleosol sequences and conclude to its aeolian origin and recording of past climates. The intensity of soil formation phases is traced through various proxies in low resolution and yet without conclusive age control. Here we review the exiting literature, available data, and interpretations from loess-palaeosol sequences in the Kashmir Valley. These are placed in the context of our own observations and loess from the Indian subcontinent.
Anatomy and Connectivity of the Subthalamic Nucleus in Humans and Non-human Primates

The Subthalamic Nucleus (STh) is an oval-shaped diencephalic structure located ventrally to the thalamus, playing a fundamental role in the circuitry of the basal ganglia. In addition to being involved in the pathophysiology of several neurodegenerative disorders, such as Huntington’s and Parkinson’s disease, the STh is one of the target nuclei for deep brain stimulation. However, most of the anatomical evidence available derives from non-human primate studies. In this review, we will present the topographical and morphological organization of the nucleus and its connections to structurally and functionally related regions of the basal ganglia circuitry. We will also highlight the importance of additional research in humans focused on validating STh connectivity, cytoarchitectural organization, and its functional subdivision.
Genetic Susceptibility to Gestational Diabetes Mellitus in a Chinese Population

Introduction: New genetic variants associated with susceptibility to obesity and metabolic diseases have been discovered in recent genome-wide association (GWA) studies. The aim of this study was to investigate the association of theses risk variants with gestational diabetes mellitus (GDM). Methods: We performed a case-control study including 964 unrelated pregnant women with GDM and 1,021 pregnant women with normal glucose tolerance (as controls). A total of 33 genetic variants confirmed by GWA studies for obesity and metabolic diseases were selected and measured. Results: We observed that FTO rs1121980 and KCNQ1 rs163182 conferred a decreased GDM risk in the dominant and additive model [additive model: OR (95% CI) = 0.79 (0.67–0.94), P = 0.007 for rs1121980; OR(95%CI) = 0.84 (0.73–0.96), P = 0.009 for rs163182], whereas MC4R rs12970134 and PROX1 rs340841 conferred an increased GDM risk in the dominant, recessive, and additive model [additive model: OR(95%CI) = 1.25 (1.07–1.46), P = 0.006 for rs12970134; OR(95%CI) = 1.22 (1.07–1.39), P = 0.002 for rs340841). With the increasing number of risk alleles of the four significant SNPs, GDM risk was significantly increased in a dose-dependent manner (P trend < 0.001). And the significant positive associations between the weighted genetic risk score and risk of GDM persisted. Further function annotation indicated that these four SNPs may fall on the functional elements of human pancreatic islets. The genotype-phenotype associations indicated that these SNPs may contribute to GDM by affecting the expression levels of their nearby or distant genes. Conclusion: Our study suggests that FTO rs1121980, KCNQ1 rs163182, MC4R rs12970134, and PROX1 rs340841 may be markers for susceptibility to GDM in a Chinese population.