Miracle-dz/UniFAR-FTUs huggingface dataset:
Responses of broilers to sodium bicarbonate supplementation of diets containing varying arginine : lysine ratios

Interactions of sodium bicarbonate (NaHCO3) with dietary arginine : lysine (arg : lys) ratios at ther- moneutral (21∞C) and high (31∞C) temperatures were investigated with 21n42-day-old broilers fed diets containing increasing concentrations of arginine to produce arg : lys ratios of 1.05, 1.15, 1.25, and 1.35, with and without 16 g NaHCO3/kg. Consistent positive relationships were observed between increasing dietary arg : lys ratios and improved food intake and weight gain at 31∞C with broilers fed diets without NaHCO3. The primary response to increasing dietary arg: lys ratio in broilers receiving NaHCO3 was increased food intake. This gave corresponding increases in weight gain at 31∞C, but not at 21∞C. Increases in dietary arg : lys ratio increased plasma arginine, ornithine, and arg:lys ratio but had little effect on plasma lysine concentrations. NaHCO3 alone had no direct effect on plasma amino acid patterns but was important in potentiating the elevated plasma arg : lys ratio responses observed at 31∞C in broilers receiving NaHCO3 in their diet. The results indicate important interrelationships exist between dietary amino acids and electrolytes, and the existence of a nutritional requirement for bicarbonate at high temperatures.
Using Bumble Bee Watch to investigate the accuracy and perception of bumble bee (Bombus spp.) identification by community scientists

Community science programs provide an opportunity to gather scientific data to inform conservation policy and management. This study examines the accuracy of community science identifications submitted to the North American Bumble Bee Watch program on a per species level and as compared to each species’ conservation status, as well as users (members of the public) and experts (those with expertise in the field of bumble bee biology) perceived ease of species identification. Photos of bumble bees (Hymenoptera: Apidae: Bombus) are submitted to the program by users and verified (species name corrected or assigned as necessary) by an expert. Over 22,000 records from over 4,900 users were used in the analyses. Accuracy was measured in two ways: percent agreement (percent of all records submitted correctly by users) and veracity (percent of all verified records submitted correctly by the users). Users generally perceived it harder to identify species than experts. User perceptions were not significantly different from the observed percent agreement or veracity, while expert perceptions were significantly different (overly optimistic) from the observed percent agreement but not the veracity. We compared user submitted names to final expert verified names and found that, for all species combined, the average percent agreement was 53.20% while the average veracity was 55.86%. There was a wide range in percent agreement values per species, although sample size and the role of chance did affect some species agreements. As the conservation status of species increased to higher levels of extinction risk, species were increasingly more likely to have a lower percent agreement but higher levels of veracity than species of least concern. For each species name submitted, the number of different species verified by experts varied from 1 to 32. Future research may investigate which factors relate to success in user identification through community science. These findings could play a role in informing the design of community science programs in the future, including for use in long-term and national-level monitoring of wild pollinators.
Identifying Rattus species using mitochondrial DNA.

In recent years, research has shown that geographical variation in mitochondrial DNA of commensal rats provides a strong signal of human dispersal and migration. However, interpretation of genetic variation is complicated by the presence of multiple species of Rattus especially in Island Southeast Asia, by the occurrence of some of these Rattus sp. as subfossils in archaeological and natural sites, and by the difficulty of osteological identification of these remains. Amplification of DNA from ancient sources usually yields only small fragments (∼ 200 bp). We assessed whether we could identify Rattus sp. reliably with DNA barcoding using cytochrome oxidase I (COI) sequences, or tree-based methods using D-loop, cytochrome b and COI sequences. Species forming well-differentiated clades in a molecular phylogeny were accurately identified by both methods, even when we used short DNA fragments. Identification was less accurate for paraphyletic and polyphyletic species. We suggest that taxonomic revisions that recognize cryptic or polytypic species will lead to even greater accuracy of DNA-based identification methods.
Matching User Preferences and Behavior for Mobility

Understanding user mobility is central to develop better transport systems that answer users' needs. Users usually plan their travel according to their needs and preferences; however, different factors can influence their choices when traveling. In this work, we model users' preferences, and we match their actual transport use. We use data coming from a mobility platform developed for mobile devices, whose aim is to understand the value of users' travel time. Our first goal is to characterize the perception that users have of their mobility by analyzing their general preferences expressed before their travel time. Our approach combines dimensionality reduction and clustering techniques to provide interpretable profiles of users. Then, we perform the same task after monitoring users' travels by doing a matching between users' preferences and their actual behavior. Our results show that there are substantial differences between users' perception of their mobility and their actual behavior: users overestimate their preferences for specific mobility modes, that in general, yield a lower return in terms of the worthwhileness of their trip.
User-level Threading

An important class of computer software, such as network servers, exhibits concurrency through many loosely coupled and potentially long-running communication sessions. For these applications, a long-standing open question is whether thread-per-session programming can deliver comparable performance to event-driven programming. This paper clearly demonstrates, for the first time, that it is possible to employ user-level threading for building threadper- session applications without compromising functionality, efficiency, performance, or scalability. We present the design and implementation of a general-purpose, yet nimble, user-level M:N threading runtime that is built from scratch to accomplish these objectives. Its key components are efficient and effective load balancing and user-level I/O blocking. While no other runtime exists with comparable characteristics, an important fundamental finding of this work is that building this runtime does not require particularly intricate data structures or algorithms. The runtime is thus a straightforward existence proof for user-level threading without performance compromises and can serve as a reference platform for future research. It is evaluated in comparison to event-driven software, system-level threading, and several other user-level threading runtimes. An experimental evaluation is conducted using benchmark programs, as well as the popular Memcached application. We demonstrate that our user-level runtime outperforms other threading runtimes and enables thread-per-session programming at high levels of concurrency and hardware parallelism without sacrificing performance.
Carpellodes or staminodes? Problems in the genus Pandanus (Pandanaceae), and their taxonomic significance

Carpellodes or staminodes? Problems in the genus Pandanus (Pandanaceae), and their taxonomic significance. The staminodes of the male flower of Pandanus palustris (section Megakeura) and the carpellodes of that of P. barklyi (section Barklya) were studied by both light microscopy and SEM. Comparison of these staminodes and carpellodes with those of the male flowers of P. androcephalanthos, P. hermaphroditus, and P. kariangensis (section Martellidendron), and with the staminodes of the male flower of P. brosimos (section Karuka) revealed that the staminodes are devoid of fibres, each having a single vascular bundle, whereas the carpellodes contain several strands of fibres, each associated with a vascular bundle. These distinctive characters are identical to those differentiating the stamens from the carpels in the genus. These staminodes and carpellodes are of taxonomic value, since they vary markedly between the species, though their main structure is similar within each section. In P. barklyi the male flower had no genuine column, and the filaments were fused to form a staminal tube.
Efficient Local Medium Access

Shah, Shin and Tetali [25] initiated the study of queuing systems on the medium access channel with arbitrary interference graph. The graph models dependencies between the channel members -- any two connected by an edge are dependent. This problem could be also re-stated as a query system with dependent elements or local scheduling of dependent packets/jobs. In short, if two dependent units, also called stations, want to transmit (or be in the same query, or do jobs in parallel), there is a conflict and none of them succeeds. The problem is particularly challenging, if the units need to make their decisions locally, without any coordination. Prior the paper by Shah, Shin and Tetali [FOCS 2011], the main focus was on the clique graph -- even in this simple topology, many problems related to stability remain open. While the solution by Shah, Shin and Tetali [FOCS 2011] is semi-local, as nodes make use of information about interfering neighbors in the graph, we provide the first purely local stable algorithms. In particular, in our algorithms stations make their decision whether to transmit or not based only on looking at their local queues. Based only on this feature, and without using a priori knowledge of topology, we design an algorithm that allows all stations for implicit transferring information to and from all other stations. We use it as a tool for developing universally stable algorithms for the problem of queuing messages -- i.e., guaranteeing bounded queues when, on average, less than one independent set is injected per round. The first one is stable in adversarial (worst-case) sense, the second one -- in stochastic sense (average-case). We also prove optimality of our algorithm in adversarial sense: no algorithm can be stable against injections with rate ρ=1 (when, on average, one independent set is injected per round). Moreover, for the class of non-adaptive protocols, we show that it is not possible to achieve stability for any injection rate Ω(1/log m), where m is the size of the largest clique in the interference graph. We extend the result by showing that such protocols are not stable on some interference graphs with no cliques of size at least 3 even for injection rates Ω(√[3](log n)/n). This result separates the model with general interference graphs from the classical model of a multiple access channel (in which the interference graph is a clique), in which there exist non-adaptive algorithms stable for adversarial injection rates O(1/log2 n).
The Impact of Oral Sodium Chloride Supplementation on Thrive and the Intestinal Microbiome in Neonates With Small Bowel Ostomies: A Prospective Cohort Study

Background: Infants with ileostomies often suffer from sodium depletion, ultimately leading to a failure to thrive. Moreover, early-infantile microbial dysbiosis may potentially aggravate weight faltering. Given that sodium supplementation has been used to restore weight gain and feeding practices largely determine infantile microbiota, the current study investigated the effect of sodium chloride (NaCl) on weight gain and intestinal microbiome in infants with jejuno- and ileostomies. Methods: A prospective cohort study including 24 neonates with enterostomies compared 19 subjects receiving oral NaCl (5.85%) to five subjects without supplementation with respect to postoperative changes in thrive and the intestinal microbiome. Results: Infants receiving NaCl after enterostomy-surgery showed vastly improved weight gain and an increased abundance of Lactobacillus in fecal samples, as compared to subjects without oral supplement who displayed decreasing percentiles for weight and did not reveal a higher abundance of probiotic strains within the ostomy effluent. Contrarily, Klebsiella was equally enriched in supplemented infants, reflecting a higher susceptibility for infections in preterm neonates. Discussion: Our findings support oral NaCl supplementation as a mainstay of postoperative treatment in infants with small bowel ostomies who are predisposed to suffer from a sodium depletion-associated failure to thrive. Not only does NaCl promote weight gain by increasing glucose resorption, but it also appears to induce microbial restoration by enhancing the abundance of health-promoting probiotic bacteria. This finding has an even greater significance when facing an elevated Klebsiella/Bifidobacteria (K/B) ratio, believed to represent an early-life microbial biomarker for development of allergic disease.
Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed and rhizosphere were collected from northeast and central-south China in two harvest years and analyzed using a metabarcoding approach targeting 16S rRNA gene region. A higher level of vertical transmission (from parent seed microbiota to offspring) was revealed, as compared to the acquisition from the rhizosphere (25.5 vs 10.7%). The core microbiota of the rice seeds consisted of a smaller proportion of OTUs (3.59%) than that of the rice rhizosphere (7.54%). Among the core microbiota, species in Arthrobacter, Bacillus, Blastococcus, Curtobacterium, Pseudomonas, and Ramlibacter have been reported as potential pathogens and/or beneficial bacteria for plants. Both the seed and the rhizosphere of rice showed distance-decay of similarity in microbial communities. Seed moisture and winter mean annual temperature (WMAT) had significant impacts on seed microbiota, while WMAT, total carbon, available potassium, available phosphorus, aluminum, pH, and total nitrogen significantly determined the rhizosphere microbiota. Multiple functional pathways were found to be enriched in the seed or the rhizosphere microbiota, which, to some extent, explained the potential adaptation of bacterial communities to respective living habitats. The results presented here elucidate the composition and possible sources of rice seed microbiota, which is crucial for the health and productivity management in sustainable agriculture.
The Role of Vector Trait Variation in Vector-Borne Disease Dynamics

Many important endemic and emerging diseases are transmitted by vectors that are biting arthropods. The functional traits of vectors can affect pathogen transmission rates directly and also through their effect on vector population dynamics. Increasing empirical evidence shows that vector traits vary significantly across individuals, populations, and environmental conditions, and at time scales relevant to disease transmission dynamics. Here, we review empirical evidence for variation in vector traits and how this trait variation is currently incorporated into mathematical models of vector-borne disease transmission. We argue that mechanistically incorporating trait variation into these models, by explicitly capturing its effects on vector fitness and abundance, can improve the reliability of their predictions in a changing world. We provide a conceptual framework for incorporating trait variation into vector-borne disease transmission models, and highlight key empirical and theoretical challenges. This framework provides a means to conceptualize how traits can be incorporated in vector borne disease systems, and identifies key areas in which trait variation can be explored. Determining when and to what extent it is important to incorporate trait variation into vector borne disease models remains an important, outstanding question.
Gray Matter Changes in the Insular Cortex During the Course of the Schizophrenia Spectrum

Progressive gray matter reductions in the insular cortex have been reported in the early phases of schizophrenia (Sz); however, the trajectory of these reductions during the course of the illness currently remains unclear. Furthermore, it has not yet been established whether patients with schizotypal (SzTypal) features exhibit progressive changes in the insular cortex. This follow-up magnetic resonance imaging study examined volume changes in the short and long insular cortices (mean inter-scan interval = 2.6 years) of 23 first-episode (FE) and 17 chronic patients with Sz, 14 with SzTypal disorder, and 21 healthy controls. Baseline comparisons revealed smaller insular cortex volumes bilaterally in Sz patients (particularly in the chronic group) than in SzTypal patients and healthy controls. FESz patients showed significantly larger gray matter reductions in the insular cortex over time (left: −3.4%/year; right: −2.9%/year) than those in healthy controls (−0.1%/year for both hemispheres) without the effect of subregion or antipsychotic medication, whereas chronic Sz (left: −1.5%/year; right: −1.6%/year) and SzTypal (left: 0.5%/year; right: −0.6%/year) patients did not. Active atrophy of the right insular cortex during FE correlated with fewer improvements in positive symptoms in the Sz groups, while mild atrophy of the left insular cortex during the chronic phase was associated with the severity of negative symptoms in the follow-up period. The present results support dynamic volumetric changes in the insular cortex being specific to overt Sz among the spectrum disorders examined and their degree and role in symptomatology appear to differ across the illness stages.
NO-Dependent Mechanisms of Myosin Heavy Chain Transcription Regulation in Rat Soleus Muscle After 7-Days Hindlimb Unloading

It is known that nitric oxide (NO) may affect myosin heavy chain (MyHC) isoform mRNA transcription in skeletal muscles. The content of NO in soleus muscles decreases during rat hindlimb unloading as well as slow MyHC mRNA transcription. We aimed to detect which signaling pathways are involved in NO-dependent prevention of hindlimb-suspension (HS)-induced changes in MyHCs’ expression pattern. Male Wistar rats were divided into four groups: cage control group (C), hindlimb suspended for 7 days (7HS), hindlimb suspended for 7 days with L-arginine administration (7HS+A) (500 mg/kg body mass), and hindlimb suspended for 7 days with both L-arginine (500 mg/kg) and NO-synthase inhibitor L-NAME administration (50 mg/kg) (7HS+A+N). L-arginine treatment during 7 days of rat HS prevented HS-induced NO content decrease and slow MyHC mRNA transcription decrease and attenuated fast MyHC IIb mRNA transcription increase; it also prevented NFATc1 nuclear content decrease, calsarcin-2 expression increase, and GSK-3β Ser 9 phosphorylation decrease. Moreover, L-arginine administration prevented the HS-induced myh7b and PGC1α mRNAs content decreases and slow-type genes repressor SOX6 mRNA transcription increase. All these slow fiber-type protective effects of L-arginine were blocked in HS+A+N group, indicating that these effects were NO-dependent. Thus, NO decrease prevention during HS restores calcineurin/NFATc1 and myh7b/SOX6 signaling.
Herbal Therapies in Functional Gastrointestinal Disorders: A Narrative Review and Clinical Implication

The pathophysiology of functional gastrointestinal disorders (FGIDs) is still unclear and various complex mechanisms have been suggested to be involved. In many cases, improvement of symptoms and quality of life (QoL) in patients with FGIDs is difficult to achieve with the single-targeted treatments alone and clinical application of these treatments can be challenging owing to the side effects. Herbal preparations as complementary and alternative medicine can control multiple treatment targets of FGIDs simultaneously and relatively safely. To date, many herbal ingredients and combination preparations have been proposed across different countries and together with a variety of traditional medicine. Among the herbal therapies that are comparatively considered to have an evidence base are iberogast (STW-5) and peppermint oil, which have been mainly studied and used in Europe, and rikkunshito and motilitone (DA-9701), which are extracted from natural substances in traditional medicine, are the focus of this review. These herbal medications have multi-target pharmacology similar to the etiology of FGIDs, such as altered intestinal sensory and motor function, inflammation, neurohormonal abnormality, and have displayed comparable efficacy and safety in controlled trials. To achieve the treatment goal of refractory FGIDs, extensive and high quality studies on the pharmacological mechanisms and clinical effects of these herbal medications as well as efforts to develop new promising herbal compounds are required.
Biomarkers Associated With Aortic Valve Calcification: Should We Focus on Sex Specific Processes?

Objective Circulating biomarkers are useful in detection and monitoring of cardiovascular diseases. However, their role in aortic valve disease is unclear. Mechanisms are rapidly elucidated and sex differences are suggested to be involved. Therefore, we sought to identify biomarkers involved in aortic valve calcification (AVC) stratified by sex. Methods Blood samples of 34 patients with AVC (without further overt cardiovascular disease, including absence of hemodynamic consequences of valvular calcification) were compared with 136 patients without AVC. AVC was determined using computed tomography calcium scoring. Circulating biomarkers were quantified using a novel antibody-based method (Olink Proseek Multiplex Cardiovascular Panel I) and 92 biomarkers were compared between patients with and without AVC. Results In the overall population, Interleukin-1 Receptor Antagonist and pappalysin-1 were associated with increased and decreased odds of having AVC. These differences were driven by the male population [IL1RA: OR 2.79 (1.16–6.70), p = 0.022; PAPPA: OR 0.30 (0.11–0.84), p = 0.021]. Furthermore, TNF-related activation-induced cytokine (TRANCE) and fibroblast growth factor-23 were associated decreased odds of having AVC, and monocyte chemotactic protein-1 was associated with increased odds of having AVC [TRANCE: OR 0.32 (0.12–0.80), p = 0.015; FGF23: OR 0.41 (0.170–0.991), p = 0.048; MCP1: OR 2.64 (1.02–6.81), p = 0.045]. In contrast, galanin peptides and ST2 were associated with increased odds of having AVC in females [GAL: OR 12.38 (1.31–116.7), p = 0.028; ST2: OR13.64 (1.21–153.33), p = 0.034]. Conclusion In this exploratory study, we identified biomarkers involved in inflammation, fibrosis and calcification which may be associated with having AVC. Biomarkers involved in fibrosis may show higher expression in females, whilst biomarkers involved in inflammation and calcification could associate with AVC in males.