Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges in upscaling laboratory studies to ecosystems in soil microbiology research

Soil microbiology has entered into the big data era, but the challenges in bridging laboratory‐, field‐, and model‐based studies of ecosystem functions still remain. Indeed, the limitation of factors in laboratory experiments disregards interactions of a broad range of in situ environmental drivers leading to frequent contradictions between laboratory‐ and field‐based studies, which may consequently mislead model development and projections. Upscaling soil microbiology research from laboratory to ecosystems represents one of the grand challenges facing environmental scientists, but with great potential to inform policymakers toward climate‐smart and resource‐efficient ecosystems. The upscaling is not only a scale problem, but also requires disentangling functional relationships and processes on each level. We point to three potential reasons for the gaps between laboratory‐ and field‐based studies (i.e., spatiotemporal dynamics, sampling disturbances, and plant–soil–microbial feedbacks), and three key issues of caution when bridging observations and model predictions (i.e., across‐scale effect, complex‐process coupling, and multi‐factor regulation). Field‐based studies only cover a limited range of environmental variation that must be supplemented by laboratory and mesocosm manipulative studies when revealing the underlying mechanisms. The knowledge gaps in upscaling soil microbiology from laboratory to ecosystems should motivate interdisciplinary collaboration across experimental, observational, theoretic, and modeling research.
LATE POSTPANCREATICODUODENECTOMY HEMORRHAGE: INCIDENCE, RISK FACTORS, MANAGEMENT AND OUTCOME

ABSTRACT Background:Postpancreaticoduodenectomy (PD) hemorrhage (PPH) is a life-threatening complication after PD. The main objective of this study was to evaluate incidence and factors associated with late PPH as well as the management strategy and outcomes. Methods: Between May 2017 and March 2020, clinical data from 192 patients undergoing PD were collected prospectively in the CHIRPAN Database (NCT02871336) and retrospectively analyzed. In our institution, all patients scheduled for a PD are routinely admitted for monitoring and management in intensive/intermediate care unit (ICU/IMC). Results: The incidence of late PPH was 17% (32 of 192), whereas the 90-day mortality rate of late PPH was 19% (6 of 32). Late PPH was associated with 90-day mortality (P = 0.001). Using multivariate analysis, independent risk factors for late PPH were postoperative sepsis (P = 0.036), and on day 3, creatinine (P = 0.025), drain fluid amylase concentration (P = 0.023), lipase concentration (P < 0.001), and C-reactive protein (CRP) concentration (P < 0.001). We developed two predictive scores for PPH occurrence, the PANCRHEMO scores. Score 1 was associated with 68.8% sensitivity, 85.6% specificity, 48.8% predictive positive value, 93.2% negative predictive value, and an area under the receiver operating characteristic curves of 0.841. Score 2 was associated with 81.2% sensitivity, 76.9% specificity, 41.3% predictive positive value, 95.3% negative predictive value, and an area under the receiver operating characteristic curve of 0.859. Conclusions: Routine ICU/IMC monitoring might contribute to a better management of these complications. Some predicting factors such as postoperative sepsis and biological markers on day 3 should help physicians to determine patients requiring a prolonged ICU/IMC monitoring.
Prestige Orientation and Reconciliation in the Workplace

Human social hierarchies comprise two distinct bases of status: dominance and prestige. One can acquire high social status not only by physically intimidating others (dominance) but also by providing information goods to others (prestige). Given that prestige-oriented individuals need to be liked and accepted by others, we hypothesized that they would be more eager to reconcile with their coworkers when they were involved in interpersonal conflicts in their workplaces. Study 1 asked 487 respondents about their conciliatory behaviors in response to workplace conflicts. Prestige-oriented individuals were more apologetic (when they hurt someone in their workplace) and forgiving (when they were hurt by someone). However, analyses of a subsample of respondents who had conflicts with their followers showed that organizational leaders’ prestige orientation was associated only with forgiveness but not with apologetic behavior. Study 2 collected comparable data from 678 organizational leaders. Study 2 confirmed the results of the subsample analysis of Study 1. Compared with leaders low in prestige orientation, leaders high in prestige orientation were more likely to forgive their subordinates; however, they were no more likely to apologize to their subordinates.
Methimazole‐induced gestational hypothyroidism affects the offspring development and differently impairs the conditioned fear in male and female adulthood rodents

Gestational hypothyroidism is a prevalent disorder in pregnant women and also impairs fetal development with relevant outcomes. One of the outcomes of greatest interest has been rodent fear‐ and anxiety‐like behavior. However, the relationship between maternal hypothyroidism and onset of conditioned fear‐related responses in offspring remains controversial. Here, we used a well‐validated methimazole‐induced gestational hypothyroidism to investigate the behavioral consequences in offspring. Dams were treated with methimazole at 0.02% in drinking water up to gestational Day 9. Maternal body weights and maternal behavior were evaluated, and the puppies ware analyzed for weight gain and physical/behavioral development and assigned for the open field and fear conditioning test. Methimazole‐induced gestational hypothyroidism induced loss in maternal and litter weight, increases in maternal behavior, and impairs in offspring developmental landmarks in both male and female rodents. Only male offspring enhanced responsiveness to conditioned fear‐like behavior in adulthood.
An evaluation of the aged mental health and primary care partnership program

Objective To evaluate the Mental Health and Primary Care Partnership (MaP) pilot program which operated in a metropolitan Melbourne setting in 2020. Method Data collection included: surveys, interviews, file audits, and an evaluation of routinely collected data, with MaP consumers, their carers, GPs, Practice Managers and Nurses located in Boroondara, and MaP and Aged Person’s Mental Health Service staff. Results Thirty-five consumers aged between 66 and 101 years old (of whom 63% were female) received support from the MaP program throughout its 12-month operation. Statistically significant improvements in outcome measures assessing for psychological distress and symptoms of mental illness were observed. Strengths of the program included the single referral pathway and the provision of services for those not meeting criteria to access tertiary mental health support. Consumers and clinicians made recommendations for service improvement including provision of a longer duration of care to consumers and greater integration of community and primary care. Conclusions It is hoped that the learnings from the MaP pilot program can be used to guide future program development.
Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner

Background: Accumulating evidence shows that N6-methyladenosine (m6A) modulators contribute to the process of chronic pain. However, the exact mechanisms of m6A writers involved in visceral hypersensitivity of Irritable bowel syndrome (IBS) remain unclear. This article aimed to reveal a new mechanism for the progression of IBS. Methods: The IBS-like model was established by neonatal colorectal distention (CRD). The relationship between m6A and circKcnk9 was analyzed by bioinformatics, immunofluorescence and RNA fluorescence in situ hybridization (FISH) assays. Visceral hypersensitivity was assessed based on the electromyography (EMG) response of the abdominal external oblique muscle to CRD. In vivo and in vitro studies (including EMG stereotactic infusion, Western blot and qRT-PCR) were utilized to explore the biological functions of related indicators. The bioinformatics, RIP experiments and RNA pull-down assays were used to explore the potential molecular mechanisms. Results: We identified that neonatal CRD increased the level of the m6A via methyltransferase-like 3 (METTL3) in the hippocampal neurons. Subsequently, knockdown of METTL3 could alleviate visceral hypersensitivity in IBS-like rats. By contrast, overexpression of METTL3 could induce visceral hypersensitivity and activate hippocampal neurons in control rats. Moreover, YTHDC1, the only m6A-associated protein predicted by bioinformatics to bind to circKcnk9, modulated visceral hypersensitivity through regulating the nuclear export of circKcnk9 in an m6A-dependent manner. Notably, FISH data suggested that the increased nuclear staining of circKcnk9 caused by siYTHDC1 could be recovered by overexpression of YTHDC1 wild type (WT) but not YTHDC1 negative control (NC) in PC12 cells. Conclusions: Our findings reveal a new regulatory mechanism in progress of IBS, that is, METTL3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner. Graphical Abstract
Competitive Transmission of Carbapenem-Resistant Klebsiella pneumoniae in a Newly Opened Intensive Care Unit

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global challenge for human health. In health care settings, patients have frequent interactions with other patients and the environment, rendering challenges for untangling the introduction and transmission of CRKP. ABSTRACT We conducted a 6-month prospective study in a newly opened ICU for high-resolution tracking of carbapenem-resistant Klebsiella pneumoniae (CRKP) through environmental surveillance, patient screening, and genome sequencing. Among all ICU patients (n = 348) screened, 3.5% carried CRKP on admission and 16.3% acquired CRKP thereafter. CRKP was not detected in the environment until 10 weeks and was then isolated from 98 of 2,989 environmental samples (3.3%). The first CRKP isolate from rectal swabs (n = 37) and the first clinical isolate (n = 8) of each patient as well as the 98 isolates from environmental were subjected to whole-genome sequencing. The 143 CRKP isolates from patients and environment samples were assigned to four sequence types, with ST11 dominating (95.8%) and further divided into 14 clones, suggesting introduction of multiple clones. Subsequent CRKP transmission was complex and dynamic with 10 clones found in multiple patients and seven also detected in the environment. Two particular ST11 clones caused extensive (≥5 rooms) and persistent (≥10 weeks) environmental contamination. Both clones were associated with patients who carried CRKP throughout their prolonged ICU stay. Such “super-contaminators” are a priority for isolation and environmental surveillance. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global challenge for human health. In health care settings, patients have frequent interactions with other patients and the environment, rendering challenges for untangling the introduction and transmission of CRKP. We conducted a prospective surveillance study in a newly opened ICU for high-resolution tracking of CRKP. Our study demonstrated the dynamic, complicated transmission of CRKP and has important findings that may help to curb its spread in health care settings. First, compliance with basic measures such as routine environment cleaning and postdischarge terminal cleaning is needed to minimize the environmental contamination-driven spread. Second, active screening could demonstrate the scale of the problem, and room transfer of patients with CRKP should be prohibited whenever possible. Third, the priority for single-room isolation should be given to patients with prolonged carriage of CRKP, especially in resource-limited settings. Good infection control practice lays a foundation for tackling multidrug-resistant organisms like CRKP.
A nondamaging electron microscopy approach to map In distribution in InGaN light-emitting diodes

Dark-field inline electron holography and, for comparison, high-resolution transmission electron microscopy are used to investigate the distribution of indium in GaN-based commercial high-efficiency green light-emitting diodes consisting of InGaN multiquantum wells (QWs). Owing to the low electron doses used in inline holography measurements; this technique allows to map the indium distribution without introducing any noticeable electron beam-induced damage which is hardly avoidable in other quantitative transmission electron microscopy methods. Combining the large field of view with a spatial resolution better than 1 nm, we show that the InGaN QWs exhibit random alloy nature without any evidence of nanometer scale gross indium clustering in the whole active region.
Differences in gut microbial fructoselysine degradation activity between breast-fed and formula-fed infants

Abstract The Amadori product fructoselysine is formed upon heating of food products and is abundantly present in infant formula while being almost absent in breast milk. The human gut microbiota can degrade fructoselysine for which interindividual differences have been described for adults. The aim of this study is to compare functional differences in microbial fructoselysine degradation between breast-fed and formula-fed infants, in view of their different diets and resulting different fructoselysine exposures. First, a publicly available metagenomic dataset with metagenome-assembled genomes (MAGs) from infant fecal samples was analyzed and showed that query genes involved in fructoselysine degradation (frlD/yhfQ) were abundantly present in multiple bacterial taxa in the fecal samples, with a higher prevalence in the formula-fed infants. Next, fecal samples collected from exclusively breast-fed and formula-fed infants were anaerobically incubated with fructoselysine. Both groups degraded fructoselysine, however the fructoselysine degradation activity was significantly higher by fecal samples from formula-fed infants. Overall, this study provides evidence that infant formula feeding, leading to increased dietary fructoselysine exposure, seems to result in an increased fructoselysine degradation activity in the gut microbiota of infants. This indicates that the infant gut microbiota adapts towards dietary fructoselysine exposure.
Body mass index and molecular subtypes of colorectal cancer

Abstract Background Obesity is an established risk factor for colorectal cancer (CRC), but the evidence for the association is inconsistent across molecular subtypes of the disease. Methods We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, and Jass classification types for 11 872 CRC cases and 11 013 controls from 11 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for covariables. Results Higher BMI was associated with increased CRC risk (OR per 5 kg/m2 = 1.18, 95% CI = 1.15 to 1.22). The positive association was stronger for men than women but similar across tumor subtypes defined by individual molecular markers. In analyses by Jass type, higher BMI was associated with elevated CRC risk for types 1-4 cases but not for type 5 CRC cases (considered familial-like/Lynch syndrome microsatellite instability-H, CpG island methylator phenotype-low or negative, BRAF-wild type, KRAS-wild type, OR = 1.04, 95% CI = 0.90 to 1.20). This pattern of associations for BMI and Jass types was consistent by sex and design of contributing studies (cohort or case-control). Conclusions In contrast to previous reports with fewer study participants, we found limited evidence of heterogeneity for the association between BMI and CRC risk according to molecular subtype, suggesting that obesity influences nearly all major pathways involved in colorectal carcinogenesis. The null association observed for the Jass type 5 suggests that BMI is not a risk factor for the development of CRC for individuals with Lynch syndrome.
Occurrence of Lagovirus europaeus (Rabbit Hemorrhagic Disease Virus) in Domestic Rabbits in Southwestern Poland in 2019: Case Report

Lagovirus europaeus (RHDV) causes a severe, highly infectious, and fatal disease in rabbits called RHD. The disease is a very serious threat to the global rabbit industry and the rabbit population in the wild. The aim of the study was to detect Lagovirus europaeus (RHDV) strains in domestic rabbits that died suddenly in Poland. The presence of RHDV was confirmed in 8 samples of all 14 samples collected. This is one of the very few reports on the existence of this virus in pet rabbits in Poland. ABSTRACT Lagovirus europaeus (rabbit hemorrhagic disease virus [RHDV]) is a small, nonenveloped, single-stranded RNA virus that causes a severe, highly infectious, and fatal disease in rabbits (Oryctolagus cuniculus) called rabbit hemorrhagic disease (RHD). Since its discovery in the 1980s, it has posed a very serious threat to the global rabbit industry and the rabbit population in the wild. According to data from 2005 to 2018, the occurrence of RHD has been reported or suspected in 50 countries, with more than one-half of the reports being recorded in European countries. The main aim of the study was to detect Lagovirus europaeus (RHDV) strains found in domestic rabbits that died suddenly in the city of Wrocław in southwest Poland. All animals (n = 14) tested in this study died naturally and showed macroscopic features at necropsy that indicated the possibility of death from RHD. As a result of the research, the presence of L. europaeus virus was confirmed in 8 samples of all 14 samples collected. All strains of Lagovirus europaeus isolated in the present study showed 100% nucleotide identity to L. europaeus GI.1 strain FRG and a strain isolated in New Zealand, as well as the L. europaeus GI.1a Erfurt strain. This suggests that it is likely that L. europaeus GI.2 strains have so far not displaced L. europaeus GI.1 strains from the environment in Poland. IMPORTANCE Lagovirus europaeus (RHDV) causes a severe, highly infectious, and fatal disease in rabbits called RHD. The disease is a very serious threat to the global rabbit industry and the rabbit population in the wild. The aim of the study was to detect Lagovirus europaeus (RHDV) strains in domestic rabbits that died suddenly in Poland. The presence of RHDV was confirmed in 8 samples of all 14 samples collected. This is one of the very few reports on the existence of this virus in pet rabbits in Poland.
Trends in cannabis use intention around the period of cannabis legalisation in Australia: An age‐period‐cohort model

Abstract Introduction This study examines age, time period and birth cohort trends in cannabis use intention and weekly use in Australia over a period in which medicinal cannabis was legalised. Methods Hierarchical age‐period‐cohort models were used to analyse the National Drug Strategy Household Survey between 2001 and 2019, including 158,395 participants aged 18–79 years. Results The hierarchical age‐period‐cohort model demonstrated a decrease in likelihood of intending to try cannabis as age increases. Similar age effects were found in intending to use cannabis as often or less often. There was broad‐based shift in attitudes for people wanting to try cannabis (2007: b = −0.51 [−0.82, −0.21]; 2019: b = 0.68 [0.38, 0.98]) or use cannabis more often (2007: b = −0.15 [−0.50, 0.20]; 2019: b = 0.83 [0.49, 1.18]). The population trend of weekly cannabis use decreased in the earlier periods but increased since 2013 (b = −0.13 [−0.25, −0.02] vs 2019: b = 0.06 [−0.09, 0.20]). This suggests that legalisation would increase uptake of cannabis and consumption among current consumers. There were distinctive inter‐generation variations: people born between 1950s and 1960s had more liberal views towards cannabis use than people born before or after (p < 0.05). There were indications that young people born in the 1990 s are catching up with the baby boomers in using cannabis more often if it was legal. Discussion and Conclusions There has been a population‐based shift in Australia in favourable attitudes towards cannabis use, more so among those born in the 1950s to 1960s than other generations. Liberal attitudes and more frequent cannabis use may put certain cohorts at higher risks of cannabis dependence and related harms.
PhraseMap: Attention-Based Keyphrases Recommendation for Information Seeking

Many Information Retrieval (IR) approaches have been proposed to extract relevant information from a large corpus. Among these methods, phrase-based retrieval methods have been proven to capture more concrete and concise information than word-based and paragraph-based methods. However, due to the complex relationship among phrases and a lack of proper visual guidance, achieving user-driven interactive information-seeking and retrieval remains challenging. In this study, we present a visual analytic approach for users to seek information from an extensive collection of documents efficiently. The main component of our approach is a PhraseMap, where nodes and edges represent the extracted keyphrases and their relationships, respectively, from a large corpus. To build the PhraseMap, we extract keyphrases from each document and link the phrases according to word attention determined using modern language models, i.e., BERT. As can be imagined, the graph is complex due to the extensive volume of information and the massive amount of relationships. Therefore, we develop a navigation algorithm to facilitate information seeking. It includes (1) a question-answering (QA) model to identify phrases related to users’ queries and (2) updating relevant phrases based on users’ feedback. To better present the PhraseMap, we introduce a resource-controlled self-organizing map (RC-SOM) to evenly and regularly display phrases on grid cells while expecting phrases with similar semantics to stay close in the visualization. To evaluate our approach, we conducted case studies with three domain experts in diverse literature. The results and feedback demonstrate its effectiveness, usability, and intelligence.
Key impact of finite-beta and fast ions in core and edge tokamak regions for the transition to advanced scenarios

Extensive linear and non-linear gyrokinetic simulations and linear magnetohydrodynamic (MHD) analyses performed for JET hybrid discharges with improved confinement have shown that the large population of fast ions found in the plasma core under particular heating conditions has a strong impact on core microturbulence and edge MHD by reducing core ion heat fluxes and increasing pedestal pressure in a feedback mechanism. In the case of the ITER like wall, it is shown how this mechanism plays a decisive role for the transition to plasma regimes with improved confinement and it can explain the weak power degradation obtained in dedicated power scans. The mechanism is found to be highly dependent on plasma triangularity as it changes the balance between the improvement in the plasma core and the edge. The feedback mechanism can play a similar role in the ITER hybrid scenario as in the JET discharges analysed due to its high triangularity plasmas and the large amount of fast ions generated in the core by the heating systems and the alpha power.