Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of size and phylogeny on patterns of covariation among life-history traits in the mammals

Do size and phylogeny affect patterns of covariation in life-history traits? If there are phylogenetic constraints on the evolution of life histories, do they differ from lineage to lineage? I applied principal component analysis and cluster analysis to two data sets 65 mammal species (14 orders, 30 families, 10 traits) and 162 mammal species (22 orders, 64 families, 6 traits). In both data sets, most of the covariation in life-history traits could be accounted for by the first two factors, and in both data sets their interpretation was similar. The first factor, accounting for 68-75% of covariation of life-history traits, ranked the animals from early maturing, small, short-lived animals with short gestation periods, many small altricial young, and long lactation periods, to the opposite suite of traits in large animals. The second factor, accounting for 12-20% of the covariation in life-history traits, ranked the animals from altricial to precocial. When order and family effects were removed, the proportion of variance accounted for by the first factor dropped 29-36%, and the number of high-level clusters increased. Analysis within individual families revealed differences from lineage to lineage in the loadings of each trait on the first two principle factors. Weight alone accounts for much of the tendency for mammals to be arranged on a single axis ranging from early maturing, highly fecund, and short-lived small animals to the opposite. However, after the effects of weight were removed, order and family effects still had significant impact on patterns of covariation. Thus morphological design, in addition to size, may constrain life-history evolution. This explains why earlier workers saw clear patterns of covariation at high taxonomic levels whereas subsequent workers have found less covariation within species.
JUST: JD Urban Spatio-Temporal Data Engine

With the prevalence of positioning techniques, a prodigious number of spatio-temporal data is generated con-stantly. To effectively support sophisticated urban applications, e.g., location-based services, based on spatio-temporal data, it is desirable for an efficient, scalable, update-enabled, and easy-to-use spatio-temporal data management system.This paper presents JUST, i.e., JD Urban Spatio-Temporal data engine, which can efficiently manage big spatio-temporal data in a convenient way. JUST incorporates the distributed NoSQL data store, i.e., Apache HBase, as the underlying storage, GeoMesa as the spatio-temporal data indexing tool, and Apache Spark as the execution engine. We creatively design two indexing techniques, i.e., Z2T and XZ2T, which accelerates spatio-temporal queries tremendously. Furthermore, we introduce a compression mechanism, which not only greatly reduces the storage cost, but also improves the query efficiency. To make JUST easy-to-use, we design and implement a complete SQL engine, with which all operations can be performed through a SQL-like query language, i.e., JustQL. JUST also supports inherently new data insertions and historical data updates without index reconstruction. JUST is deployed as a PaaS in JD with multi-users support. Many applications have been developed based on the SDKs provided by JUST. Extensive experiments are carried out with six state-of-the-art distributed spatio-temporal data management systems based on two real datasets and one synthetic dataset. The results show that JUST has a competitive query performance and is much more scalable than them.
Prevalence of Elbow Joint Arthritis and Enthesitis in Rheumatoid Arthritis

Objectives: The prevalence of elbow joint arthritis in rheumatoid arthritis (RA) assessed by ultrasound has not yet been investigated. Methods: We investigated 102 patients with RA and 50 patients without rheumatological disease. Both elbow joints were examined by ultrasound for effusion, hypervascularization, and enthesitis. A clinical examination was performed, and Disease Activity Score in 28 joints (DAS28), and visual analog scale for pain (VASp) were recorded. Arthritis was defined as joint effusion (≥grade II) and synovial hyperperfusion. Results: The RA cohort versus the control group displayed a joint effusion in 54.9% vs. 6.9%, a hypervascularization in 6.8% vs. 0%. Arthritis was detected in 36 RA patients (35.29%) and no one in the control group. Four (3.8%) RA patients and one (1%) control displayed enthesitis. The RA cohort showed a significant correlation between movement restriction and joint effusion (p-value = 0.001) as well as DAS28 (p-value = 0.02) and between DAS28 and ultrasound detected arthritis (p-value = 0.022). In an overall analysis, a highly significant correlation of VASp with movement restriction (MR) (p-value ≤ 0.001), the presence of joint effusion (p-value ≤ 0.001), and the diagnosis of RA (p-value ≤ 0.001) were observed. Interrater analysis of ultrasound imaging showed good agreement with Cohen’s kappa of 0.896. Conclusion: The prevalence of elbow arthritis in RA seems to be high, with 35.29%. Movement restriction is a good indicator, but not in all RA patients (32 vs. 70 patients without MR) compared to the control group (5 vs. 45 patients without MR). Reported pain correlates with joint effusion and MR (p-value ≤ 0.001).
Coping Styles in Pregnancy, Their Demographic and Psychological Influences, and Their Association with Postpartum Depression: A Longitudinal Study of Women in China

We aimed to investigate the coping styles of Chinese pregnant women, identify factors associated with coping and further explore the effect of coping during pregnancy on postpartum depression. A longitudinal study was performed from early pregnancy to six-week postpartum. A total of 1126 women were recruited by convenience sampling and participants who completed eight questionnaires at four time points were included (three self-developed questionnaires, Coping Style Questionnaire, Generalized Anxiety Disorder-7, Brief Resilience Scale, Rosenberg Self-esteem Scale, Edinburgh Postnatal Depression Scale) (n = 615). Linear regression analyses were used to identify the possible factors for coping and their association with postpartum depression. The mean scores of positive coping and negative coping were 2.03 and 1.21, respectively. Women with a higher educational level scored higher on both positive and negative coping in pregnancy. Resilience was associated with both positive and negative coping, while self-esteem only related to positive coping (p < 0.05). Postpartum depression was associated with both positive and negative coping (p < 0.05). The women in our study reported using positive coping styles more than negative coping antenatally. Positive and negative coping behaviors could be used simultaneously. Increasing self-esteem and resilience antenatally might promote more positive coping and further reduce the occurrence of postpartum depression.
Using Nonpolio Enterovirus Detection to Assess the Integrity of Stool Specimens Collected From Acute Flaccid Paralysis Cases in Somalia During 2014-2017.

Background Despite insecurity challenges in Somalia, key indicators for acute flaccid paralysis (AFP) surveillance have met recommended targets. However, recent outbreaks of vaccine-derived polioviruses have raised concerns about possible gaps. We analyzed nonpolio enterovirus (NPEV) and Sabin poliovirus isolation rates to investigate whether comparing these rates can inform about the integrity of stool specimens from inaccessible areas and the likelihood of detecting circulating polioviruses. Methods Using logistic regression, we analyzed case-based AFP surveillance data for 1348 cases with onset during 2014-2017. We assessed the adjusted impacts of variables including age, accessibility, and Sabin-like virus isolation on NPEV detection. Results NPEVs were more likely to be isolated from AFP case patients reported from inaccessible areas than accessible areas (23% vs 15%; P = .01). In a multivariable model, inaccessibility and detection of Sabin-like virus were positively associated with NPEV detection (adjusted odds ratio [AOR], 1.75; 95% confidence interval [CI], 1.14-2.65; and AOR, 1.79; 95% CI, 1.07-2.90; respectively), while being aged ≥5 years was negatively associated (AOR, 0.42; 95% CI, 0.20-0.85). Conclusions Rates of NPEV and Sabin poliovirus detection in inaccessible areas suggest that the integrity of fecal specimens tested for AFP surveillance in Somalia can generate useful AFP data, but uncertainties remain about surveillance system quality.
Lactobacillus casei addition to a repletion diet-induced early normalisation of cytokine profils during a pneumococcal infection in malnourished mice

Abstract This work studied the influence of Lactobacillus casei on cytokine production during repletion of malnourished mice in the face of an infectious challenge. In addition, the number and function of cells involved in the immune response against a respiratory infection was evaluated. Weaned mice were malnourished after consuming a protein-free diet (PFD) for 21 days. Malnourished mice were fed a balanced conventional diet (BCD) for 7 days or BCD for 7 days with L. casei supplementation on day 6 and day 7 (BCD+Lc). The malnourished control group (MNC) received PFD while the well-nourished control (WNC) mice consumed BCD. Mice were challenged intranasally with Streptococcus pneumoniae at the end of each dietary treatment. Malnutrition impaired the levels of serum tumor necrosis factor (TNF)-α and interleukin (IL)-1β, IL-4, IL-6 and IL-10. In addition, neutrophil number and activity, lymphocyte maturation and bone marrow CD4+, CD8+ and CD19+ cells number, were also impaired in the MNC group. Repletion with BCD induced a slight improvement in some of the parameters studied. However, when L. casei was added to the BCD, a normalisation of TNF-α, IL-1β and IL-6 values after infection and an increase in the levels of IL-10 and IL-4 compared to the WNC group was observed. Moreover, BCD+Lc induced a significant improvement in blood and bone marrow cells. Consequently, the use of L. casei as a supplement in a repletion diet was associated with a pattern of inflammatory and anti-inflammatory cytokines that led to an increased number and functionality of the cells that participate in the immune response against a pneumococcal infection.
The evolution of the type VI secretion system as a disintegration weapon

The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well understood. Here we present a new agent-based model that enables detailed study of the evolutionary costs and benefits of T6SS weaponry during competition with other bacteria. Our model identifies a key problem with the T6SS. Because of its short range, T6SS activity becomes self-limiting, as dead cells accumulate in its way, forming “corpse barriers” that block further attacks. However, further exploration with the model presented a solution to this problem: if injected toxins can quickly lyse target cells in addition to killing them, the T6SS becomes a much more effective weapon. We tested this prediction with single-cell analysis of combat between T6SS-wielding Acinetobacter baylyi and T6SS-sensitive Escherichia coli. As predicted, delivery of lytic toxins is highly effective, whereas nonlytic toxins leave large patches of E. coli alive. We then analyzed hundreds of bacterial species using published genomic data, which suggest that the great majority of T6SS-wielding species do indeed use lytic toxins, indicative of a general principle underlying weapon evolution. Our work suggests that, in the T6SS, bacteria have evolved a disintegration weapon whose effectiveness often rests upon the ability to break up competitors. Understanding the evolutionary function of bacterial weapons can help in the design of probiotics that can both establish well and eliminate problem species.
Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms

The human hookworm Necator americanus infects more than 400 million people worldwide, contributing substantially to the poverty in these regions. Adult stage N. americanus live in the small intestine of the human host where they inject excretory/secretory (ES) products into the mucosa. ES products have been characterized at the proteome level for a number of animal hookworm species, but until now, the difficulty in obtaining sufficient live N. americanus has been an obstacle in characterizing the secretome of this important human pathogen. Herein we describe the ES proteome of N. americanus and utilize this information along with RNA Seq data to conduct the first proteogenomic analysis of a parasitic helminth, significantly improving the available genome and thereby generating a robust description of the parasite secretome. The genome annotation resulted in a revised prediction of 3,425 fewer genes than initially reported, accompanied by a significant increase in the number of exons and introns, total gene length and the percentage of the genome covered by genes. Almost 200 ES proteins were identified by LC-MS/MS with SCP/TAPS proteins, ‘hypothetical’ proteins and proteases among the most abundant families. These proteins were compared to commonly used model species of human parasitic infections, including Ancylostoma caninum, Nippostrongylus brasiliensis and Heligmosomoides polygyrus. SCP/TAPS proteins are immunogenic in nematode infections, so we expressed four of those identified in this study in recombinant form and showed that they are all recognized to varying degrees by serum antibodies from hookworm-infected subjects from a disease-endemic area of Brazil. Our findings provide valuable information on important families of proteins with both known and unknown functions that could be instrumental in host-parasite interactions, including protein families that might be key for parasite survival in the onslaught of robust immune responses, as well as vaccine and diagnostic targets.
Diversification rate vs. diversification density: Decoupled consequences of plant height for diversification of Alooideae in time and space

While biodiversity hotspots are typically identified on the basis of species number per unit area, their exceptional richness is often attributed, either implicitly or explicitly, to high diversification rates. High species concentrations, however, need not reflect rapid diversification, with the diversity of some hotspots accumulating at modest rates over long timespans. Here we explore the relationship between diversification in time vs. diversification in space and develop the concept of diversification density to describe the spatial scale of species accumulation in a clade. We investigate how plant height is associated with both aspects of diversification in Alooideae, a large plant subfamily with its center of diversity in the Greater Cape Floristic Region. We first reconstruct a time-calibrated phylogeny for Alooideae and demonstrate an evolutionary tendency towards reduced plant height. While plant height does not correlate with diversification rate across Alooideae it does so with diversification per unit space: clades of small plants tend to have the highest diversification densities. Furthermore, we find that diversification in time vs. space are uncorrelated. Our results show that diversification rate and density can be decoupled, and suggest that while some biodiversity hotspots might have been generated by high diversification rates, others are the product of high diversification density.
Potential Therapeutic Targeting of Coronavirus Spike Glycoprotein Priming

Processing of certain viral proteins and bacterial toxins by host serine proteases is a frequent and critical step in virulence. The coronavirus spike glycoprotein contains three (S1, S2, and S2′) cleavage sites that are processed by human host proteases. The exact nature of these cleavage sites, and their respective processing proteases, can determine whether the virus can cross species and the level of pathogenicity. Recent comparisons of the genomes of the highly pathogenic SARS-CoV2 and MERS-CoV, with less pathogenic strains (e.g., Bat-RaTG13, the bat homologue of SARS-CoV2) identified possible mutations in the receptor binding domain and in the S1 and S2′ cleavage sites of their spike glycoprotein. However, there remains some confusion on the relative roles of the possible serine proteases involved for priming. Using anthrax toxin as a model system, we show that in vivo inhibition of priming by pan-active serine protease inhibitors can be effective at suppressing toxicity. Hence, our studies should encourage further efforts in developing either pan-serine protease inhibitors or inhibitor cocktails to target SARS-CoV2 and potentially ward off future pandemics that could develop because of additional mutations in the S-protein priming sequence in coronaviruses.
IDENTIFICATION OF CULTURES OF WOOD-INHABITING HYMENOMYCETES

A multiple-choice key for the identification of cultures of 149 species of wood-inhabiting Hymenomycetes, whose cultural characters have been published previously, is based on the following diagnostic characters: presence or absence of extracellular oxidase, types of septation of hyphae, occurrence of special structures and accessory spores, color of hyphae and mycelial mats, color changes in agar, rates of growth, formation of fruit bodies, odor, host relationships, and interfertility phenomena. In the key, each diagnostic character is symbolized by a number, the Code Symbol; each species is described in abbreviated form by a Species Code, the series of Code Symbols that denote the characters shown by the species; and each section in the key is headed by its Key Code, the series of Code Symbols that denote the characters shared by all the species in the section. Most of the final sections in the key consist of a number of species with identical or similar Species Codes. In these sections, detailed descri.
Role of a Brief Intensive Observation Area with a Dedicated Team of Doctors in the Management of Acute Heart Failure Patients: A Retrospective Observational Study

Background and objectives: Acute heart failure (AHF) is one of the main causes of hospitalization in Western countries. Usually, patients cannot be admitted directly to the wards (access block) and stay in the emergency room. Holding units are clinical decision units, or observation units, within the ED that are able to alleviate access block and to contribute to a reduction in hospitalization. Observation units have also been shown to play a role in specific clinical conditions, like the acute exacerbation of heart failure. This study aimed to analyze the impact of a brief intensive observation (OBI) area on the management of acute heart failure (AHF) patients. The OBI is a holding unit dedicated to the stabilization of unstable patients with a team of dedicated physicians. Materials and Methods: We conducted a retrospective and single-centered observational study with retrospective collection of the data of all patients who presented to our emergency department with AHF during 2017. We evaluated and compared two cohorts of patients, those treated in the OBI and those who were not, in terms of the reduction in color codes at discharge, mortality rate within the emergency room (ER), hospitalization rate, rate of transfer to less intensive facilities, and readmission rate at 7, 14, and 30 days after discharge. Results: We enrolled 920 patients from 1st January to 31st December. Of these, 61% were transferred to the OBI for stabilization. No statistically significant difference between the OBI and non-OBI populations in terms of age and gender was observed. OBI patients had worse clinical conditions on arrival. The patients treated in the OBI had longer process times, which would be expected, to allow patient stabilization. The stabilization rate in the OBI was higher, since presumably OBI admission protected patients from “worse condition” at discharge. Conclusions: Data from our study show that a dedicated area of the ER, such as the OBI, has progressively allowed a change in the treatment path of the patient, where the aim is no longer to admit the patient for processing but to treat the patient first and then, if necessary, admit or refer. This has resulted in very good feedback on patient stabilization and has resulted in a better management of beds, reduced admission rates, and reduced use of high intensity care beds.
Octopamine: A new feeding modulator in Lymnaea

The role of octopamine (OA) in the feeding system of the pond snail, Lymnaea stagnalis, was studied by applying behavioural tests on intact animals, and a combination of electrophysiological analysis and morphological labelling in the isolated central nervous system. OA antagonists phentolamine, demethylchlordimeform (DCDM) and 2-chloro-4-methyl-2-(phenylimino)-imidazolidine (NC-7) were injected into intact snails and the sucrose-induced feeding response of animals was monitored. Snails that received 25 to 50 mg kg-1 phentolamine did not start feeding in sucrose, and the same dose of NC-7 reduced the number of feeding animals by 80 to 90% 1 to 3 hours after injection. DCDM treatment reduced feeding by 20 to 60%. In addition, both phentolamine and NC-7 significantly decreased the feeding rate of those animals that still accepted food after 1 to 6 hours of injection. In the central nervous system a pair of buccal neurons was identified by electrophysiological and morphological criteria. After double labelling (intracellular staining with Lucifer yellow followed by OA-immunocytochemistry) these neurons were shown to be OA immunoreactive, and electrophysiological experiments confirmed that they are members of the buccal feeding system. Therefore the newly identified buccal neurons were called OC neurons (putative octopamine containing neurons or octopaminergic cells). Synchronous intracellular recordings demonstrated that the OC neurons share a common rhythm with feeding neurons either appearing spontaneously or evoked by intracellularly stimulated feeding interneurons. OC neurons also have synaptic connections with identified members of the feeding network: electrical coupling was demonstrated between OC neurons and members of the B4 cluster motoneurons, furthermore, chemically transmitted synaptic responses were recorded both on feeding motoneurons (B1, B2 cells) and the SO modulatory interneuron after the stimulation of OC neurons. However, elementary synaptic potentials could not be recorded on the follower cells of OC neurons. Prolonged (20 to 30 s) intracellular stimulation of OC cells activated the buccal feeding neurons leading to rhythmic activity pattern (fictive feeding) in a way similar to OA applied by perfusion onto isolated central nervous system (CNS) preparations. Our results suggest that OA acts as a modulatory substance in the feeding system of Lymnaea stagnalis and the newly identified pair of OC neurons belongs to the buccal feeding network.