Miracle-dz/UniFAR-FTUs huggingface dataset:
Soil hydraulic properties in one‐dimensional layered soil profile using layer‐specific soil moisture assimilation scheme

We developed a layer‐specific soil‐moisture assimilation scheme using a simulation‐optimization framework, Soil‐Water‐Atmosphere‐Plant model with genetic algorithm (SWAP‐GA). Here, we explored the quantification of the soil hydraulic properties in a layered soil column under various combinations of soil types, vegetation covers, bottom boundary conditions and soil layering using idealized (synthetic) numerical studies and actual field experiments. We demonstrated that soil layers and vertical heterogeneity (layering arrangements) could impact to the uncertainty of quantifying soil hydraulic parameters. We also found that, under layered soil system, when the subsurface flows are dominated by upward fluxes, e.g., from a shallow water table, the solution to the inverse problem appears to be more elusive. However, when the soil profile is predominantly draining, the soil hydraulic parameters could be fairly estimated well across soil layers, corroborating the results of past studies on homogenous soil columns. In the field experiments, the layer‐specific assimilation scheme successfully matched soil moisture estimates with observations at the individual soil layers suggesting that this approach could be applied in real world conditions.
Are brown trout replacing or displacing bull trout populations in a changing climate

Understanding how climate change may facilitate species turnover is an important step in identifying potential conservation strategies. We used data from 33 sites in western Montana to quantify climate associations with native bull trout (Salvelinus confluentus) and non-native brown trout (Salmo trutta) abundance and population growth rates (λ). We estimated λ using exponential growth state-space models and delineated study sites based on bull trout use for either spawning and rearing (SR) or foraging, migrating, and overwintering (FMO) habitat. Bull trout abundance was negatively associated with mean August stream temperatures within SR habitat (r = −0.75). Brown trout abundance was generally highest at temperatures between 12 and 14 °C. We found bull trout λ were generally stable at sites with mean August temperature below 10 °C but significantly decreasing, rare, or extirpated at 58% of the sites with temperatures exceeding 10 °C. Brown trout λ were highest in SR and sites with temperatures exceeding 1.
Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient

Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function; however, our understanding of alpine soil ecology remains limited. This study aimed to (i) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to (ii) assess the impact of woody shrub expansion on these patterns. In the White Mountains of California, sagebrush (Artemisia rothrockii) shrubs have been expanding upwards into alpine areas since 1960. In this study, we combined observational field data with a manipulative shrub removal experiment along an elevation transect of alpine shrub expansion. We utilized next‐generation sequencing of the ITS1 region for fungi and joint distribution modelling to tease apart effects of the environment and intracommunity interactions on soil fungi. We found that soil fungal diversity declines and community composition changes with increasing elevation. Both abiotic factors (primarily soil moisture and soil organic C) and woody sagebrush range expansion had significant effects on these patterns. However, fungal diversity and relative abundance had high spatial variation, overwhelming the predictive power of vegetation type, elevation and abiotic soil conditions at the landscape scale. Finally, we observed positive and negative associations among fungal taxa which may be important in structuring community responses to global change.
Influence of physical exercise on microRNAs in skeletal muscle regeneration, aging and diseases

Skeletal muscle is a dynamic tissue with remarkable plasticity and its growth and regeneration are highly organized, with the activation of specific transcription factors, proliferative pathways and cytokines. The decline of skeletal muscle tissue with age, is one of the most important causes of functional loss of independence in older adults. Maintaining skeletal muscle function throughout the lifespan is a prerequisite for good health and independent living. Physical activity represents one of the most effective preventive agents for muscle decay in aging. Several studies have underlined the importance of microRNAs (miRNAs) in the control of myogenesis and of skeletal muscle regeneration and function. In this review, we reported an overview and recent advances about the role of miRNAs expressed in the skeletal muscle, miRNAs regulation by exercise in skeletal muscle, the consequences of different physical exercise training modalities in the skeletal muscle miRNA profile, their regulation under pathological conditions and the role of miRNAs in age-related muscle wasting. Specific miRNAs appear to be involved in response to different types of exercise and therefore to play an important role in muscle fiber identity and myofiber gene expression in adults and elder population. Understanding the roles and regulation of skeletal muscle miRNAs during muscle regeneration may result in new therapeutic approaches in aging or diseases with impaired muscle function or re-growth.
Variability in cannibalism in Northeast Arctic cod (Gadus morhua) during the period 1947–2006

Abstract Cannibalism is probably the most important and also the most variable cause of natural mortality for age 1–4 Northeast Arctic cod. Also, the proportion of cod in the diet of Northeast Arctic cod increases with increasing size of the predatory cod. For this stock, long time series describing diet composition are available (qualitative stomach content data for 1947–2005 and quantitative data for 1984–2006). These data were analysed together with survey indices for young cod and abundance of capelin, the most important prey item for cod. The abundance of age 1–3 cod indicated by the survey indices and the abundance of young cod in cod stomachs are well correlated. An inverse relationship between mortality induced by cannibalism and capelin abundance was found. Cannibalism was at a high level from 1947 to 1965 and then again in the mid-1990s. The high level of cannibalism in the mid-1990s was comparable to that observed in the 1950s. It is outlined how the qualitative and quantitative stomach content data could be combined to include cannibalism in the estimates of cod abundance back to 1947.
Cold electron and ion beams generated from trapped atoms

A novel way of creating low-temperature electron and ion beams is demonstrated. The beams are generated by converting a laser-cooled atom cloud to a highly excited Rydberg gas, which subsequently develops into an ultracold plasma. Charged particles are extracted from the Rydberg gas and the plasma by a pulsed electric field. The properties of the resulting electron and ion pulses are experimentally studied. Pulses of a few hundred ns duration containing a few pC of charge were observed. Upper limits for the temperature of such beams (60K for ions and 500K for electrons) are obtained, and the beams are shown to have low emittance. Further development of the method may lead to the generation of high-brightness charged-particle beams from ultracold plasmas.
Redox Processes and Water Quality of Selected Principal Aquifer Systems

Reduction/oxidation (redox) conditions in 15 principal aquifer (PA) systems of the United States, and their impact on several water quality issues, were assessed from a large data base collected by the National Water‐Quality Assessment Program of the USGS. The logic of these assessments was based on the observed ecological succession of electron acceptors such as dissolved oxygen, nitrate, and sulfate and threshold concentrations of these substrates needed to support active microbial metabolism. Similarly, the utilization of solid‐phase electron acceptors such as Mn(IV) and Fe(III) is indicated by the production of dissolved manganese and iron. An internally consistent set of threshold concentration criteria was developed and applied to a large data set of 1692 water samples from the PAs to assess ambient redox conditions. The indicated redox conditions then were related to the occurrence of selected natural (arsenic) and anthropogenic (nitrate and volatile organic compounds) contaminants in ground water. For the natural and anthropogenic contaminants assessed in this study, considering redox conditions as defined by this framework of redox indicator species and threshold concentrations explained many water quality trends observed at a regional scale. An important finding of this study was that samples indicating mixed redox processes provide information on redox heterogeneity that is useful for assessing common water quality issues. Given the interpretive power of the redox framework and given that it is relatively inexpensive and easy to measure the chemical parameters included in the framework, those parameters should be included in routine water quality monitoring programs whenever possible.
Topic Modeling of Short Texts: A Pseudo-Document View

Recent years have witnessed the unprecedented growth of online social media, which empower short texts as the prevalent format for information of Internet. Given the nature of sparsity, however, short text topic modeling remains a critical yet much-watched challenge in both academy and industry. Rich research efforts have been put on building different types of probabilistic topic models for short texts, among which the self aggregation methods without using auxiliary information become an emerging solution for providing informative cross-text word co-occurrences. However, models along this line are still rarely seen, and the representative one Self-Aggregation Topic Model (SATM) is prone to overfitting and computationally expensive. In light of this, in this paper, we propose a novel probabilistic model called Pseudo-document-based Topic Model (PTM) for short text topic modeling. PTM introduces the concept of pseudo document to implicitly aggregate short texts against data sparsity. By modeling the topic distributions of latent pseudo documents rather than short texts, PTM is expected to gain excellent performance in both accuracy and efficiency. A Sparsity-enhanced PTM (SPTM for short) is also proposed by applying Spike and Slab prior, with the purpose of eliminating undesired correlations between pseudo documents and latent topics. Extensive experiments on various real-world data sets with state-of-the-art baselines demonstrate the high quality of topics learned by PTM and its robustness with reduced training samples. It is also interesting to show that i) SPTM gains a clear edge over PTM when the number of pseudo documents is relatively small, and ii) the constraint that a short text belongs to only one pseudo document is critically important for the success of PTM. We finally take an in-depth semantic analysis to unveil directly the fabulous function of pseudo documents in finding cross-text word co-occurrences for topic modeling.
Optimal Expectations

This paper introduces a tractable, structural model of subjective beliefs. Forward-looking agents care about expected future utility flows, and hence have higher current felicity if they believe that better outcomes are more likely. On the other hand, biased expectations lead to poorer decisions and worse realized outcomes on average. Optimal expectations balance these forces by maximizing average felicity. A small bias in beliefs typically leads to first-order gains due to increased anticipatory utility and only to second-order costs due to distorted behavior. We show that in a portfolio choice problem, agents overestimate the return on their investment and exhibit a preference for skewness. In general equilibrium, agents' prior beliefs are endogenously heterogeneous. Finally, in a consumption-saving problem with stochastic income, agents are both overconfident and overoptimistic.
A case report and literature review

Rationale: Behçet disease (BD) is a recurrent vasculitis characterized by oral and genital mucous membrane ulcers, uveitis, and skin lesions but only rarely leg ulcers. To our knowledge, no efficacious therapy has been described for BD patients with complicating, destructive leg ulcers. Patient concerns: Here, We report the case of a 55-year-old woman with generalized erythema nodosum-like, papulopustular lesions, recurrent oral and genital ulcers accompanied with recurrent leg ulcers and trouble walking. Diagnoses: Based upon the patient’s clinical feature and positive pathergy test , BD was confirmed. Interventions: Conventional immunosuppressive therapy and anti-tumor necrosis factor inhibitors, adalimumab and etanercept, had no demonstrable clinical effect. Mesenchymal stem cell (MSC) injection combined with low-dose prednisone and thalidomide, however, completely ameliorated the ulcers on one leg, significantly improved ulcers on the other leg, and returned normal function to both legs. Outcomes: The ulcerative lesions remained in remission, and the affected leg functioned normally after 34 months’ follow-up. Lessons: Our experience suggests that MSC infusion might be a potentially successful therapy for intractable drug-resistant BD patients with concomitant leg ulcer. Abbreviations: ANCA = anti-neutrophil cytoplasmic antibodies, AZA = azathioprine, BD = Behçet disease, CTX = cyclophosphamide, ISG = International Study Group, MSC = mesenchymal stem cell, MTX= methotrexate, RA = rheumatoid arthritis, SLE = systemic lupus erythematosus, SSc = systemic sclerosis, TNF = tumor necrosis factor.
Function of pectoral fins in rainbow trout: behavioral repertoire and hydrodynamic forces

SUMMARY Salmonid fishes (trout, salmon and relatives) have served as a model system for study of the mechanics of aquatic animal locomotion, yet little is known about the function of non-axial propulsors in this major taxonomic group. In this study we examine the behavioral and hydromechanical repertoire of the paired pectoral fins of rainbow trout Oncorhynchus mykiss, performing both steady rectilinear swimming and unsteady maneuvering locomotion. A combination of kinematic analysis and quantitative flow visualization (using digital particle image velocimetry) enables identification of the propulsive roles played by pectoral fin motions. During constant-speed swimming (0.5 and 1.0 body length s-1), the pectoral fins remain adducted against the body. These fins are actively recruited, however, for a variety of maneuvering behaviors, including station holding in still water (hovering), low-speed (i.e. non-fast-start) turning, and rapid deceleration of the body during braking. Despite having a shallow pectoral-fin base orientation (the plesiomorphic teleost condition), trout are capable of rotating the fin base over 30° during maneuvering, which affords the fin an impressive degree of kinematic versatility. When hovering, the pectoral fins are depressed beneath the body and twisted along their long axes to allow anteroposterior sculling. During turning and braking, the fins undergo spanwise rotation in the opposite direction and exhibit mediolateral and dorsoventral excursions. Water velocity fields and calculated momentum flows in the wake of the pectoral fins reveal that positive thrust is not generated during maneuvering, except during the retraction half-stroke of hovering. Relatively large laterally directed fluid force (mean 2.7 mN) is developed during turning, whose reaction powers yawing rotation of the body (4-41° s-1). During deceleration, the wake-force line of action falls below the center of mass of the body, and this result supports a long-standing mechanical model of braking by fishes with ventrally positioned paired fins. Despite its traditional categorization as a propulsor of limited functional importance, the salmoniform pectoral fin exhibits a diverse locomotor repertoire comparable to that of higher teleostean fishes.
Determinants of Severity in Acute Pancreatitis: A Nation-wide Multicenter Prospective Cohort Study.

OBJECTIVE The aim of this study was to compare and validate the different classifications of severity in acute pancreatitis (AP) and to investigate which characteristics of the disease are associated with worse outcomes. SUMMARY OF BACKGROUND DATA AP is a heterogeneous disease, ranging from uneventful cases to patients with considerable morbidity and high mortality rates. Severity classifications based on legitimate determinants of severity are important to correctly describe the course of disease. METHODS A prospective multicenter cohort study involving patients with AP from 23 hospitals in Spain. The Atlanta Classification (AC), Revised Atlanta Classification (RAC), and Determinant-based Classification (DBC) were compared. Binary logistic multivariate analysis was performed to investigate independent determinants of severity. RESULTS A total of 1655 patients were included; 70 patients (4.2%) died. RAC and DBC were equally superior to AC for describing the clinical course of AP. Although any kind of organ failure was associated with increased morbidity and mortality, persistent organ failure (POF) was the most significant determinant of severity. All local complications were associated with worse outcomes. Infected pancreatic necrosis correlated with high morbidity, but in the presence of POF, it was not associated to higher mortality when compared with sterile necrotizing pancreatitis. Exacerbation of previous comorbidity was associated with increased morbidity and mortality. CONCLUSION The RAC and DBC both signify an advance in the description and differentiation of AP patients. Herein, we describe the complications of the disease independently associated to morbidity and mortality. Our findings are valuable not only when designing future studies on AP but also for the improvement of current classifications.
Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes.

Positive Darwinian selection at the molecular level is often studied by comparing the number of synonymous nucleotide substitutions per synonymous site (d,) and the number of nonsynonymous substitutions per nonsynonymous site (dN) between homologous gene sequences, and a t-test with an infinite number of degrees of freedom is usually used for determining the statistical significance of the difference between ds and dN (Hughes and Nei 1988; Kumar, Tamura, and Nei 1993). An assumption required for this test is that the sample size (number of substitutions between the sequences) is so large that ds and dN are approximately normally distributed. However, it is unclear how well the t-test performs when the sample size is small and whether there is a better way of testing positive selection. In this letter, we address these issues by using a recently published data set of primate lysozyme sequences (Messier and Stewart 1997) as an example. where SE(ds) and SE(d,) are the standard errors of ds and dN, respectively. In this case, the test statistic (t,) becomes
The nuclear retinoid‐related orphan receptor ROR α controls circadian thermogenic programming in white fat depots

The RORα‐deficient staggerer (sg/sg) mouse is lean and resistant to diet‐induced obesity. Its thermogenic activity was shown to be increased not only in brown adipose tissue (BAT), but also in subcutaneous white adipose tissue (WAT) where UCP1 content was enhanced, however, without Prdm16 coexpression. Our observation of partial multilocular lipid morphology of WAT in sg/sg mice both in the inguinal and perigonadal sites led us to focus on the phenotype of both fat depots. Because RORα is a nuclear factor acting in the clock machinery, we looked at the circadian expression profile of genes involved in thermogenesis and browning in WAT and BAT depots of sg/sg and WT mice, through real‐time quantitative PCR and western blotting. This 24‐h period approach revealed both a rhythmic expression of thermogenic genes in WAT and an increased browning of all the WAT depots tested in sg/sg mice that indeed involved the canonical browning process (through induction of Pgc‐1α and Prdm16). This was associated with an enhanced isoproterenol‐induced oxygen consumption rate of WAT explants from sg/sg mice, which was reproducible in WT explants by treatment with a RORα inverse agonist SR 3335, that induced a parallel increase in the UCP1 protein. Inhibitors of browning differentiation, such as TLE3 and RIP140, could be new targets of RORα that would be rather implicated in the whitening of adipocytes. Our study showed the pivotal role of RORα as an inhibitor of the thermogenic program in WAT, the role that could be counteracted in vivo with the RORα antagonists currently in development.
Epidemiological study of Intestinal Parasitosis in rural area of Nepal.

Intestinal parasitosis is one of the major public health and socio-economic problems in Nepal. It is ranked among the top10 morbidities in Nepal. Fecal samples were collected from the patients attending to different hospitals and privatelaboratories throughout the Myagdi district. A total of 985 participants were included in the study. The age ranged from 1to 86 years. Commonly affected age group was of below 15 years. Male to female ratio was 1.3:1. The general prevalence of infection with different types of intestinal parasites was 14.7% (145). The fecal examination revealed different types of helminths (7.2%) and protozoan (7.5%). Giardia lamblia was the most common parasite (5.5%), followed by Entamoeba histolytica 2.0%, Ascaris lumbricoides 4.0%, Hookworm 1.8%, Trichuris trichiura 0.8%, Hymenolepis nana 0.4% and Taenia spp 0.2%. Multiple parasites were observed in 11 samples. Higher prevalence rates of parasitic infections were seen among children.