Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of Succession in Natural Communities and Their Role in Community Stability and Organization

The sequence of species observed after a relatively large space is opened up is a consequence of the following mechanisms. "Opportunist" species with broad dispersal powers and rapid growth to maturity usually arrive first and occupy empty space. These species cannot invade and grow in the presence of adults of their own or other species. Several alternative mechanisms may then determine which species replace these early occupants. Three models of such mechanisms have been proposed. The first "facilitation" model suggests that the entry and growth of the later species is dependent upon the earlier species "preparing the ground"; only after this can later species colonize. Evidence in support of this model applies mainly to certain primary successions and in heterotrophic succession. A second "tolerance" model suggests that a predictable sequence is produced by the existence of species that have evolved different strategies for exploiting resources. Later species will be those able to tolerate lower levels of resources than earlier ones. Thus they can invade and grow to maturity in the presence of those that preceded them. At present there exists little evidence in support of this model. A third "inhibition" model suggests that all species resist invasions of competitors. The first occupants preempt the space and will continue to exclude or inhibit later colonists until the former die or are damaged, thus releasing resources. Only then can later colonists reach maturity. A considerable body of evidence exists in support of this model. In the majority of natural communities succession is frequently interrupted by major disturbances, such as fires, storms, insect plagues, etc., starting the process all over again. However, if not interrupted, it eventually reaches a stage in which further change is on a small scale as individuals die and are replaced. The pattern of these changes will depend upon whether individuals are more likely to be replaced by a member of their own or another species. If the former, stability will be assured. However, in terrestrial communities, conditions in the soil in the immediate vicinity of long-lived plants may become modified in such a way that offspring of the same species are much less favored than those of other species. A likely cause is the buildup of host-specific pathogenic soil organisms near a long-lived plant. In this case, the species at each local site keep changing, producing local instability. Whether the average species composition of the whole tract does not change, exhibiting global stability, or whether it keeps changing has not yet been decided for any natural community.
Arsenic species in rice and rice-based products consumed by toddlers in Switzerland

ABSTRACT Inorganic arsenic (iAs) is a contaminant present in food, especially in rice and rice-based products. Toxicity of arsenic compounds (As) depends on species and oxidative state. iAs species, such as arsenite (As(III)) and arsenate (As(V)), are more bioactive and toxic than organic arsenic species, like methylarsonic acid (MMA(V)) and dimethylarsinic acid (DMA(V)) or arsenosugars and arsenobetaine. An ion chromatography-inductively coupled-plasma-mass spectroscopy method was developed to separate the four following arsenic anions: As(III), As(V), MMA(V) and DMA(V). Sample preparation was done in mild acidic conditions to ensure species preservation. The predominant arsenic species found in rice and rice-based products, except for rice drinks, was As(III), with 60–80% of the total As content, followed by DMA(V) and As(V). MMA(V) was measured only at low levels (<3%). Analyses of rice products (N = 105) intended for toddlers, including special products destined for infants and toddlers, such as dry form baby foods (N = 12) or ready-to-use form (N = 9), were done. It was found in this study that there is little or no margin of exposure. Risk assessment, using the occurrence data and indicated intake scenarios compared to reference BMDLs as established by EFSA, demonstrated toddlers with a high consumption of rice based cereals and rice drinks are at risk of high iAs exposure, for which a potential health risk cannot be excluded.
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns – a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses.
Parallel detection of lactobacillus and bacterial vaginosis-associated bacterial DNA in the chorioamnion and vagina of pregnant women at term

Abstract Background: The majority of early preterm births are associated with intrauterine infections, which are thought to occur when microbes traffic into the uterus from the lower genital tract and seed the placenta. Bacterial vaginosis (BV) is associated with heterogeneous bacterial communities in the vagina and is linked to preterm birth. The extent to which trafficking into the uterus of normal and BV-associated vaginal bacteria occurs is unknown. The study objective was to characterize in parallel the distribution and quantities of bacteria in the vagina, uterus, and placental compartments. Methods: Pregnant women at term (≥37 weeks) presenting for delivery were recruited prospectively. Swabs were collected in parallel from the vagina, chorioamnion. Choriodecidual swabs were collected if a cesarean section was performed. Samples were analyzed by culture, broad-range 16S rRNA gene PCR, and bacterial species-specific quantitative PCR (qPCR) for DNA from Lactobacillus and a panel of BV-associated bacteria. Results were correlated with placental histopathology. Results: Of the 23 women enrolled, 15 were delivered by cesarean section (N = 10 without labor; N = 5 in labor) and eight were delivered vaginally. BV was diagnosed in two women not in labor. Placental histopathology identified chorioamnionitis or funisitis in six cases [1/10 (10%) not in labor; 5/13 (38%) in labor]. Among non-laboring women, broad-range 16S qPCR detected bacteria in the chorioamnion and the choriodecidua (4/10; 40%). Among laboring women, Lactobacillus species were frequently detected in the chorioamnion by qPCR (4/13; 31%). In one case, mild chorioamnionitis was associated with qPCR detection of similar microbes in the chorioamnion and vagina (e.g. Leptotrichia/Sneathia, Megasphaera), along a quantitative gradient. Conclusions: Microbial trafficking of lactobacilli and fastidious bacteria into the chorioamniotic membranes and choriodecidua occurs at term in normal pregnancies. In one case, we demonstrated a quantitative gradient between multiple bacterial species in the lower genital tract and placenta. Not all bacterial colonization is associated with placental inflammation and clinical sequelae. Further studies of the role of placental colonization with Lactobacillus in normal pregnancy and fastidious bacteria in chorioamnionitis may improve prevention and treatment approaches for preterm labor.
Shared trauma reality in war: Mental health therapists’ experience

Introduction Shared traumatic reality occurs when therapists are doubly exposed to a traumatic event, both through their clients’ experience, along with their own direct exposure. Studies have shown that a shared traumatic reality can lead to both positive and negative outcomes for therapists. Most studies have examined these reactions sometime after the end of the traumatic event, and less is known about reactions that occur during a traumatic event. In addition, most studies have assumed, rather than examined, indirect exposure. In this study, we extend this literature by examining direct and indirect exposure of therapists during a war situation, and their psychological reactions. Method Over a period of two months in 2014, 70% of the Israeli population was exposed to rocket fire. Geographical areas differed in terms of amount of exposure, and its potential danger. 151 therapists living throughout Israel were assessed via an Internet based survey in the middle of the war, and were assessed for the effects on their professional and personal lives, degree of burnout, ways of coping and symptoms levels of PTSD and psychological distress. Results These indicate that significant differences in direct exposure occurred depending on place of residence. PTSD levels were related to higher direct exposure, as well as prior trauma exposure, but not to indirect exposure. Indirect exposure, as measured by increased workload, was related to increased distress and emotional exhaustion. Discussion These data shed light on the effects of direct and indirect exposure to a shared traumatic experience of war amongst therapists. The data support previous studies showing a greater effect of direct exposure on PTSD. Since indirect exposure appears to negatively impact burnout and psychological distress, rather than PTSD, this study shows that symptoms other than PTSD should be the result of in a shared traumatic reality.
Proteomic Analysis of Kiwifruit in Response to the Postharvest Pathogen, Botrytis cinerea

Gray mold, caused by the fungus Botrytis cinerea, is the most significant postharvest disease of kiwifruit. In the present study, iTRAQ with LC-ESI-MS/MS was used to identify the kiwifruit proteins associated with the response to B. cinerea. A total of 2,487 proteins in kiwifruit were identified. Among them, 292 represented differentially accumulated proteins (DAPs), with 196 DAPs having increased, and 96 DAPs having decreased in accumulation in B. cinerea-inoculated vs. water-inoculated, control kiwifruits. DAPs were associated with penetration site reorganization, cell wall degradation, MAPK cascades, ROS signaling, and PR proteins. In order to examine the corresponding transcriptional levels of the DAPs, RT-qPCR was conducted on a subset of 9 DAPs. In addition, virus-induced gene silencing was used to examine the role of myosin 10 in kiwifruit, a gene modulating host penetration resistance to fungal infection, in response to B. cinerea infection. The present study provides new insight on the understanding of the interaction between kiwifruit and B. cinerea.
Decreasing mortality and changes in treatment patterns in patients with acromegaly from a nationwide study.

CONTEXT New therapeutic strategies have developed for the management of acromegaly over recent decades. Whether this has improved mortality has not been fully elucidated. OBJECTIVE The primary aim was to investigate mortality in a nationwide unselected cohort of patients with acromegaly. Secondary analyses included time trends in mortality and treatment patterns. DESIGN A total of 1089 patients with acromegaly were identified in Swedish National Health Registries between 1987 and 2013. To analyse time trends, the cohort was divided into three periods (1987-1995, 1996-2004 and 2005-2013) based on the year of diagnosis. MAIN OUTCOME MEASURES Using the Swedish population as reference, standardized mortality ratios (SMRs) were calculated with 95% confidence intervals (CIs). RESULTS Overall SMR was 2.79 (95% CI: 2.43-3.15) with 232 observed and 83 expected deaths. Mortality was mainly related to circulatory diseases (SMR: 2.95, 95% CI: 2.35-3.55), including ischemic heart disease (2.00, 1.35-2.66) and cerebrovascular disease (3.99, 2.42-5.55) and malignancy (1.76, 1.27-2.26). Mortality decreased over time, with an SMR of 3.45 (2.87-4.02) and 1.86 (1.04-2.67) during the first and last time period, respectively (P = .015). During the same time periods, the frequency of pituitary surgery increased from 58% to 72% (P < 0.001) and the prevalence of hypopituitarism decreased from 41% to 23% (P < 0.001). CONCLUSIONS Excess mortality was found in this nationwide cohort of patients with acromegaly, mainly related to circulatory and malignant diseases. Although still high, mortality significantly declined over time. This could be explained by the more frequent use of pituitary surgery, decreased prevalence of hypopituitarism and the availability of new medical treatment options.
The poor outcome of second primary oral squamous cell carcinoma is attributed to Bmi1 upregulation

Radiotherapy for nasopharyngeal carcinoma has been reported to cause second primary oral squamous cell carcinoma (s‐OSCC). The prognosis and pathologic characteristic of s‐OSCC are largely unknown. Bmi1 was associated with the repair of radiation‐induced DNA damage, suggesting its possible involvement in the pathologic process of s‐OSCC. Herein, we compared the prognosis between s‐OSCC and primary OSCC (p‐OSCC) and explored the involvement of Bmi1 in s‐OSCC development. In this retrospective study, s‐OSCC and p‐OSCC patients were matched by propensity scores. Their outcomes were compared by univariate and multivariate analyses. The expression of Bmi1 in s‐OSCC and p‐OSCC was detected by immunohistochemistry (IHC). Radiation‐induced Bmi1 alteration in early‐stage was explored in a rat model and HaCaT cells. After matching, 116 pairs of patients with highly balanced characteristics were included. In univariate analysis, the overall survival (OS), disease‐specific survival (DSS), and local recurrence‐free survival (LRFS) were poorer in s‐OSCC than in p‐OSCC (P < 0.05), while their regional metastasis‐free survival (RMFS) was parallel (P = 0.112). Multivariate analysis further revealed that radiotherapy history was an independent risk factor for OS, DSS, and LRFS (P < 0.05). IHC results showed that the positive rate of Bmi1 was higher in s‐OSCC (P = 0.0027). In a rat model of radiotherapy‐induced mucositis, Bmi1 upregulation was observed 8 days after irradiation. Consistently, Bmi1 was upregulated in HaCaT cells 1 h after irradiation, and its upregulation was in accord with X‐ray exposure duration. In conclusion, the prognosis of s‐OSCC is poorer as compared to p‐OSCC, which may be attributed to Bmi1 upregulation.
Externalizing Behaviors and Callous-Unemotional Traits: Different Associations With Sleep Quality

Study Objectives Sleep quality is associated with different aspects of psychopathology, but relatively little research has examined links between sleep quality and externalizing behaviors or callous‐unemotional traits. We examined: (1) whether an association exists between sleep quality and externalizing behaviors; (2) whether anxiety mediates this association; (3) whether callous‐unemotional traits are associated with sleep quality. Methods Data from two studies were used. Study 1 involved 1556 participants of the G1219 study aged 18‐27 years (62% female). Questionnaire measures assessed sleep quality, anxiety, externalizing behaviors, and callous‐unemotional traits. Study 2 involved 338 participants aged 18‐66 years (65% female). Questionnaires measured sleep quality, externalizing behaviors, and callous‐unemotional traits. In order to assess objective sleep quality, actigraphic data were also recorded for a week from a subsample of study 2 participants (n = 43). Results In study 1, poorer sleep quality was associated with greater externalizing behaviors. This association was partially mediated by anxiety and moderated by levels of callous‐unemotional traits. There was no significant relationship between sleep quality and callous‐unemotional traits. In study 2, poorer sleep quality, as assessed via self‐reported but not objective measures, was associated with higher levels of externalizing behaviors. Furthermore, in study 2, better sleep quality (indicated in both questionnaires and actigraphy measures: lower mean activity, and greater sleep efficiency) was associated with higher levels of callous‐unemotional traits. Conclusions Self‐reports of poorer sleep quality are associated with externalizing behaviors, and this association is partially mediated by anxiety. Callous‐unemotional traits are not associated with poor sleep and may even be related to better sleep quality. This is an exceptional finding given that poor sleep quality appears to be a characteristic of most psychopathology.
A morphogram for silica‐witherite biomorphs and its application to microfossil identification in the early earth rock record

Archean hydrothermal environments formed a likely site for the origin and early evolution of life. These are also the settings, however, were complex abiologic structures can form. Low‐temperature serpentinization of ultramafic crust can generate alkaline, silica‐saturated fluids in which carbonate–silica crystalline aggregates with life‐like morphologies can self‐assemble. These “biomorphs” could have adsorbed hydrocarbons from Fischer–Tropsch type synthesis processes, leading to metamorphosed structures that resemble carbonaceous microfossils. Although this abiogenic process has been extensively cited in the literature and has generated important controversy, so far only one specific biomorph type with a filamentous shape has been discussed for the interpretation of Archean microfossils. It is therefore critical to precisely determine the full distribution in morphology and size of these biomorphs, and to study the range of plausible geochemical conditions under which these microstructures can form. Here, a set of witherite‐silica biomorph synthesis experiments in silica‐saturated solutions is presented, for a range of pH values (from 9 to 11.5) and barium ion concentrations (from 0.6 to 40 mmol/L BaCl2). Under these varying conditions, a wide range of life‐like structures is found, from fractal dendrites to complex shapes with continuous curvature. The size, spatial concentration, and morphology of the biomorphs are strongly controlled by environmental parameters, among which pH is the most important. This potentially limits the diversity of environments in which the growth of biomorphs could have occurred on Early Earth. Given the variety of the observed biomorph morphologies, our results show that the morphology of an individual microstructure is a poor criterion for biogenicity. However, biomorphs may be distinguished from actual populations of cellular microfossils by their wide, unimodal size distribution. Biomorphs grown by diffusion in silica gel can be differentiated by their continuous gradient in size, spatial density, and morphology along the direction of diffusion.
The geographical distribution of grey wolves (Canis lupus) in China: a systematic review

The grey wolf (Canis lupus) is one of the most widely distributed terrestrial mammals, and its distribution and ecology in Europe and North America are largely well described. However, the distribution of grey wolf in southern China is still highly controversial. Several well-known western literatures stated that there are no grey wolves in southern China, while the presence of grey wolf across China has been indicated in A Guide to the Mammals of China, published by Princeton University Press. It is essential to solve this discrepancy since dogs may have originated from grey wolfs in southern China. Therefore, we systematically investigated Chinese literatures about wild animal surveys and identified more than 100 articles and books that included information of the distribution of grey wolves in China. We also surveyed the collections of three Chinese natural museums and found 26 grey wolf skins specimens collected across China. Moreover, we investigated the fossil records of wolf in China and identified 25 archaeological sites with wolf remains including south China. In conclusion, with the comprehensive summary of Chinese literatures, museum specimens and fossil records, we demonstrate that grey wolves does distribute across all parts of the Chinese mainland, including the most southern parts of China.
Newborn genetic screening for spinal muscular atrophy in the UK: The views of the general population

Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder and a leading genetic cause of infant death worldwide. However, there is no routine screening program for SMA in the UK. Lack of treatments and the inability of screening tests to accurately predict disease severity are among the key reasons implementation of screening has faltered in the UK. With the recent release of the first therapy for SMA (Nusinersen), calls are being made for a reconsideration of this stance; however, very little is known about the views of the general public.
Injuries in Dutch elite field hockey players: A prospective cohort study

This study describes the prevalence, incidence density, severity, and nature of injuries in elite field hockey players over the Dutch 2015–2016 season. Eighty players answered a baseline questionnaire and were subsequently followed up every 2 weeks to report the hours spent on training/competition and experienced injuries, which were registered using the Oslo Sports Trauma Research Centre Questionnaire on Health Problems. Of the 74 players included in the analysis, 52 (70%) reported 112 injuries. Eighty‐seven injuries (78%) received medical attention, and 56 (50%) led to training/competition time‐loss. Thirty‐four injuries (30%) hampered players’ availability to train and compete. Most of the injuries (74%) were not caused by any contact. The mean prevalence of injury was 29% (95% confidence interval [CI] 3–55) for all, 9% (95% CI 0–20) for acute, and 14% (95% CI 0–36) for overuse injuries. Players sustained 3.5 (95% CI 2.5–4.5) new acute injuries per 1000 hours of training and 12.3 (95% CI 7.6–17.0) per 1000 hours of competition. The median of the severity score was 28 from 100 (25%–75% interquartile range [IQR] 16–42) for all, 35 (IQR 23–53) for acute, and 21 (IQR 16–31) for overuse injuries. On average, 1 in 4 elite field hockey players experiences an injury within a 2‐week period during the season. Although acute injuries are common, overuse injuries pose a comparable problem in elite field hockey. As injuries are a burden on players’ health and may hamper performance and availability to train and compete, prevention is of great importance.