Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Interactions Drive Distinct Taxonomic and Potential Metabolic Responses to Habitats in Karst Cave Ecosystem

In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. ABSTRACT The geological role of microorganisms has been widely studied in the karst cave ecosystem. However, microbial interactions and ecological functions in such a dark, humid, and oligotrophic habitat have received far less attention, which is crucial to understanding cave biogeochemistry. Herein, microorganisms from weathered rock and sediment along the Heshang Cave depth were analyzed by random matrix theory-based network and Tax4Fun functional prediction. The results showed that although the cave microbial communities have spatial heterogeneity, differential habitats drove the community structure and diversity. Actinobacteria were predominant in weathered rock, whereas Proteobacteria dominated the sediment. The sediment communities presented significantly higher alpha diversities due to the relatively abundant nutrition from the outside by the intermittent stream. Consistently, microbial interactions in sediment were more complex, as visualized by more nodes and links. The abundant taxa presented more positive correlations with other community members in both of the two networks, indicating that they relied on promotion effects to adapt to the extreme environment. The keystones in weathered rock were mainly involved in the biodegradation of organic compounds, whereas the keystone Nitrospira in sediment contributed to carbon/nitrogen fixation. Collectively, these findings suggest that microbial interactions may lead to distinct taxonomic and functional communities in weathered rock and sediment in the subsurface Heshang Cave. IMPORTANCE In general, the constant physicochemical conditions and limited nutrient sources over long periods in the subsurface support a stable ecosystem in karst cave. Previous studies on cave microbial ecology were mostly focused on community composition, diversity, and the relationship with local environmental factors. There are still many unknowns about the microbial interactions and functions in such a dark environment with little human interference. Two representative habitats, including weathered rock and sediment in Heshang Cave, were selected to give an integrated insight into microbial interactions and potential functions. The cooccurrence network, especially the subnetwork, was used to characterize the cave microbial interactions in detail. We demonstrated that abundant taxa primarily relied on promotion effects rather than inhibition effects to survive in Heshang Cave. Keystone species may play important metabolic roles in sustaining ecological functions. Our study provides improved understanding of microbial interaction patterns and community ecological functions in the karst cave ecosystem.
Identification of a Region in Shigella flexneri WzyB Disrupting the Interaction with WzzpHS2

Complex polysaccharide chains are synthesized by bacteria, usually at a regulated number of repeating units, which has broad implications for bacterial pathogenesis. One example is the O antigen (Oag) component of lipopolysaccharide that is predominantly synthesized by the Wzy-dependent pathway. ABSTRACT Shigella flexneri can synthesize polysaccharide chains having complex sugars and a regulated number of repeating units. S. flexneri lipopolysaccharide O antigen (Oag) is synthesized by the Wzy-dependent pathway, which is the most common pathway used in bacteria for polysaccharide synthesis. The inner membrane protein WzyB polymerizes the Oag repeat units into chains, while the polysaccharide copolymerases WzzB and WzzpHS2 determine the average number of repeat units or “the modal length,” termed short type and very long type. Our data show for the first time a direct interaction between WzyB and WzzpHS2, with and without the use of the chemical cross-linker dithiobis (succinimidyl propionate) (DSP). Additionally, mutations generated via random and site-directed mutagenesis identify a region of WzyB that caused diminished function and significantly decreased very long Oag chain polymerization, and that affected the aforementioned interaction. These results provide insight into the mechanisms underlying the regulation of Oag biosynthesis. IMPORTANCE Complex polysaccharide chains are synthesized by bacteria, usually at a regulated number of repeating units, which has broad implications for bacterial pathogenesis. One example is the O antigen (Oag) component of lipopolysaccharide that is predominantly synthesized by the Wzy-dependent pathway. Our findings show for the first time a direct physical interaction between WzyB and WzzpHS2. Additionally, a set of Wzy mutant constructs were generated, revealing a proposed active site/switch region involved in the activity of WzyB and the physical interaction with WzzpHS2. Combined, these findings further understanding of the Wzy-dependent pathway. The identification of a novel interaction with the polysaccharide copolymerase WzzpHS2 and the region of WzyB that is involved in this aforementioned interaction and its impact on WzyB Oag synthesis activity have significant implication for the prevention/treatment of bacterial diseases and discovery of novel biotechnologies.
RhoA- and Cdc42-induced antagonistic forces underlie symmetry breaking and spindle rotation in mouse oocytes

Mammalian oocyte meiotic divisions are highly asymmetric and produce a large haploid gamete and 2 small polar bodies. This relies on the ability of the cell to break symmetry and position its spindle close to the cortex before anaphase occurs. In metaphase II–arrested mouse oocytes, the spindle is actively maintained close and parallel to the cortex, until fertilization triggers sister chromatid segregation and the rotation of the spindle. The latter must indeed reorient perpendicular to the cortex to enable cytokinesis ring closure at the base of the polar body. However, the mechanisms underlying symmetry breaking and spindle rotation have remained elusive. In this study, we show that spindle rotation results from 2 antagonistic forces. First, an inward contraction of the cytokinesis furrow dependent on RhoA signaling, and second, an outward attraction exerted on both sets of chromatids by a Ran/Cdc42-dependent polarization of the actomyosin cortex. By combining live segmentation and tracking with numerical modeling, we demonstrate that this configuration becomes unstable as the ingression progresses. This leads to spontaneous symmetry breaking, which implies that neither the rotation direction nor the set of chromatids that eventually gets discarded are biologically predetermined.
Hemodynamic phenotyping of transgenic rats with ubiquitous expression of an angiotensin-(1-7)-producing fusion protein.

Activation of the angiotensin (Ang) converting enzyme 2/Ang-(1-7)/MAS receptor pathway of the renin-angiotensin system induces protective mechanisms in different diseases. Herein, we describe the cardiovascular phenotype of a new transgenic rat line (TG7371) that expresses an Ang-(1-7)-producing fusion protein. The transgene-specific mRNA and the corresponding protein were shown to be present in all evaluated tissues of TG7371 with the highest expression in aorta and brain. Plasma Ang-(1-7) levels, measured by radioimmunoassay were similar to control SD rats, however high Ang-(1-7) levels were found in the hypothalamus. TG7371 showed lower baseline mean arterial pressure, assessed in conscious or anesthetized rats by telemetry or short-term recordings, associated with increased plasma ANP and higher urinary sodium concentration. Evaluation of regional blood flow and hemodynamic parameters with fluorescent microspheres showed a significant increase in blood flow in different tissues (kidneys, mesentery, muscle, spleen, brown fat, heart and skin), with a resulting decreased total peripheral resistance. TG7371 rats also presented increased cardiac and global sympathetic tone, increased plasma AVP levels and decreased free water clearance. Altogether, our data show that expression of an Ang-(1-7)-producing fusion protein induced a hypotensive phenotype due to widespread vasodilation and consequent fall in peripheral resistance. This phenotype was associated with an increase in ANP together with an increase in AVP and sympathetic drive, which did not fully compensate the lower BP. Here we present the hemodynamic impact of long-term increase in tissue expression of an Ang-(1-7)-fusion protein and provide a new tool to investigate this peptide in different pathophysiological conditions.
Reliable Sensory Processing in Mouse Visual Cortex through Cooperative Interactions between Somatostatin and Parvalbumin Interneurons

Intrinsic neuronal variability significantly limits information encoding in the primary visual cortex (V1). However, under certain conditions, neurons can respond reliably with highly precise responses to the same visual stimuli from trial to trial. This suggests that there exists intrinsic neural circuit mechanisms that dynamically modulate the intertrial variability of visual cortical neurons. Here, we sought to elucidate the role of different inhibitory interneurons (INs) in reliable coding in mouse V1. To study the interactions between somatostatin-expressing interneurons (SST-INs) and parvalbumin-expressing interneurons (PV-INs), we used a dual-color calcium imaging technique that allowed us to simultaneously monitor these two neural ensembles while awake mice, of both sexes, passively viewed natural movies. SST neurons were more active during epochs of reliable pyramidal neuron firing, whereas PV neurons were more active during epochs of unreliable firing. SST neuron activity lagged that of PV neurons, consistent with a feedback inhibitory SST→PV circuit. To dissect the role of this circuit in pyramidal neuron activity, we used temporally limited optogenetic activation and inactivation of SST and PV interneurons during periods of reliable and unreliable pyramidal cell firing. Transient firing of SST neurons increased pyramidal neuron reliability by actively suppressing PV neurons, a proposal that was supported by a rate-based model of V1 neurons. These results identify a cooperative functional role for the SST→PV circuit in modulating the reliability of pyramidal neuron activity. SIGNIFICANCE STATEMENT Cortical neurons often respond to identical sensory stimuli with large variability. However, under certain conditions, the same neurons can also respond highly reliably. The circuit mechanisms that contribute to this modulation remain unknown. Here, we used novel dual-wavelength calcium imaging and temporally selective optical perturbation to identify an inhibitory neural circuit in visual cortex that can modulate the reliability of pyramidal neurons to naturalistic visual stimuli. Our results, supported by computational models, suggest that somatostatin interneurons increase pyramidal neuron reliability by suppressing parvalbumin interneurons via the inhibitory SST→PV circuit. These findings reveal a novel role of the SST→PV circuit in modulating the fidelity of neural coding critical for visual perception.
Language statistical learning responds to reinforcement learning principles rooted in the striatum

Statistical learning (SL) is the ability to extract regularities from the environment. In the domain of language, this ability is fundamental in the learning of words and structural rules. In lack of reliable online measures, statistical word and rule learning have been primarily investigated using offline (post-familiarization) tests, which gives limited insights into the dynamics of SL and its neural basis. Here, we capitalize on a novel task that tracks the online SL of simple syntactic structures combined with computational modeling to show that online SL responds to reinforcement learning principles rooted in striatal function. Specifically, we demonstrate—on 2 different cohorts—that a temporal difference model, which relies on prediction errors, accounts for participants’ online learning behavior. We then show that the trial-by-trial development of predictions through learning strongly correlates with activity in both ventral and dorsal striatum. Our results thus provide a detailed mechanistic account of language-related SL and an explanation for the oft-cited implication of the striatum in SL tasks. This work, therefore, bridges the long-standing gap between language learning and reinforcement learning phenomena.
Delay in the induction of labour process: a retrospective cohort study and computer simulation of maternity unit workload

Objectives Delay in the induction of labour (IOL) process is associated with poor patient experience and adverse perinatal outcome. Our objective was to identify factors associated with delay in the IOL process and develop interventions to reduce delay. Design and settings We performed a retrospective cohort study of maternity unit workload in a large UK district general hospital. Electronic hospital records were used to quantify delay in the IOL process and linear regression analysis was performed to assess significant associations between delay and potential causative factors. A novel computer maternity unit simulation model, MUMSIM (Maternity Unit Management SIMulation), was developed using real-world data and interventions were tested to identify those associated with a reduction in delay. Participants All women giving birth at Stoke Mandeville Hospital, Buckinghamshire National Health Service (NHS) Trust in 2018 (n=4932). Primary outcome measure Delay in the IOL process of more than 12 hours. Results The retrospective analysis of real-world maternity unit workload showed 30% of women had IOL and of these, 33% were delayed >12 hours with 20% delayed >24 hours, 10% delayed >48 hours and 1.3% delayed >72 hours. Delay was significantly associated with the total number of labouring women (p=0.008) and the number of booked IOL (p=0.009) but not emergency IOL, spontaneously labouring women or staffing shortfall. The MUMSIM computer simulation predicted that changing from slow release 24-hour prostaglandin to 6-hour prostaglandin for primiparous women would reduce delay by 4% (p<0.0001) and that additional staffing interventions could significantly reduce delay up to 17.9% (p<0.0001). Conclusions Planned obstetric workload of booked IOL is associated with delay rather than the unpredictable workload of women in spontaneous labour or emergency IOL. We present a novel maternity unit computer simulation model, MUMSIM, which allows prediction of the impact of interventions to reduce delay.
Clumps and Rings of Ejecta in SNR 0540–69.3 as Seen in 3D

The distribution of ejecta in young supernova remnants offers a powerful observational probe of their explosions and progenitors. Here we present a 3D reconstruction of the ejecta in SNR 0540-69.3, which is an O-rich remnant with a pulsar wind nebula located in the LMC. We use observations from the Very Large Telescope (VLT)/MUSE to study Hβ, [O iii] λ λ4959, 5007, Hα, [S ii] λ λ6717, 6731, [Ar iii] λ7136, and [S iii] λ9069. This is complemented by 2D spectra from VLT/X-shooter, which also cover [O ii] λ λ3726, 3729, and [Fe ii] λ12567. We identify three main emission components: (i) clumpy rings in the inner nebula (≲1000 km s−1) with similar morphologies in all lines; (ii) faint extended [O iii] emission dominated by an irregular ring-like structure with radius ∼1600 km s−1 and inclination ∼40°, but with maximal velocities reaching ∼3000 km s−1; and (iii) a blob of Hα and Hβ located southeast of the pulsar at velocities ∼1500–3500 km s−1. We analyze the geometry using a clump-finding algorithm and use the clumps in the [O iii] ring to estimate an age of 1146 ± 116 yr. The observations favor an interpretation of the [O iii] ring as ejecta, while the origin of the H-blob is more uncertain. An alternative explanation is that it is the blown-off envelope of a binary companion. From the detection of Balmer lines in the innermost ejecta we confirm that SNR 0540 was a Type II supernova and that hydrogen was mixed down to low velocities in the explosion.
Gynura procumbens ethanol extract improves vascular dysfunction by suppressing inflammation in postmenopausal rats fed a high-fat diet

Abstract Context Gynura procumbens (Lour.) Merr. (Asteraceae) has been reported to have various pharmacological activities including anti-inflammatory effects. Objective This study sought to determine whether Gynura procumbens (GP) could improve vascular reactivity by suppressing inflammation in postmenopausal rats fed with five-times heated palm oil (5HPO) diet. Materials and methods Forty-eight female Sprague-Dawley rats were randomly divided into sham [non-ovariectomized; grouped as control, GP extracts (250 and 500 mg/kg), atorvastatin (ATV, 10 mg/kg)] and postmenopausal (PM) groups [ovariectomized rats fed with 5HPO; grouped as PM, GP extracts (250 and 500 mg/kg) and ATV (10 mg/kg)]. Each group (n = 6) was either supplemented with GP extract or ATV orally once daily for 6 months. Results In comparison with the untreated PM group, 250 and 500 mg/kg GP supplementation to PM groups reduced the systolic blood pressure (103 ± 2.7, 86 ± 2.4 vs. 156 ± 7.83 mmHg, p < 0.05), intima-media thickness (101.28 ± 3.4, 93.91 ± 2.93 vs. 143.78 ± 3.31 µM), vasoconstriction percentage induced by phenylephrine (102.5%, 88.3%, vs. 51.8%), sICAM-1 (0.49, 0.26 vs. 0.56 pg/mL) and sVCAM-1 (0.39, 0.25 vs. 0.45 pg/mL). GP extract supplementation increased vasorelaxation percentage induced by acetylcholine (78.4% vs. 47.3%) and sodium nitroprusside (84.2% vs. 53.7%), increased changes in plasma nitric oxide level (1.25%, 1.31% vs. 1.9%), and suppressed the elevation of TNF-α (0.39 vs. 1.02 pg/mL), IL-6 (0.43 vs. 0.77 pg/mL) and CRP (0.29 vs. 0.69 ng/mL) in the PM groups. Conclusions GP extract might improve vascular dysfunction by suppressing the inflammatory response, consequently preventing blood pressure elevation.
Hi, my name is Martha: Using names to measure and mitigate bias in generative dialogue models

All AI models are susceptible to learning biases in data that they are trained on. For generative dialogue models, being trained on real human conversations containing unbalanced gender and race/ethnicity references can lead to models that display learned biases, which we define here broadly as any measurable differences in the distributions of words or semantic content of conversations based on demographic groups. We measure the strength of such biases by producing artificial conversations between two copies of a dialogue model, conditioning one conversational partner to state a name commonly associated with a certain gender and/or race/ethnicity. We find that larger capacity models tend to exhibit more gender bias and greater stereotyping of occupations by gender. We show that several methods of tuning these dialogue models, specifically name scrambling, controlled generation, and unlikelihood training, are effective in reducing bias in conversation, including on a downstream conversational task. Name scrambling is also effective in lowering differences in token usage across conversations where partners have names associated with different genders or races/ethnicities.
Forget me not: A Gentle Reminder to Mind the Simple Multi-Layer Perceptron Baseline for Text Classification

Graph neural networks have triggered a resurgence of graph-based text classiﬁcation. We show that already a simple MLP baseline achieves comparable performance on benchmark datasets, questioning the importance of synthetic graph structures. When considering an inductive scenario, i. e. , when adding new documents to a corpus, a simple MLP even outperforms most graph-based models. We further ﬁne-tune DistilBERT for comparison and ﬁnd that it outperforms all state-of-the-art models. We suggest that future studies use at least an MLP baseline to contextualize the re-sults. We provide recommendations for the de-sign and training of such a baseline.
The Risk of Cutaneous Squamous Cell Carcinoma Among Patients with Type 2 Diabetes Receiving Hydrochlorothiazide: A Cohort Study

Background: Because of continuous hyperglycemia and hyperinsulinemia and the use of photosensitizing drug, hydrochlorothiazide (HCTZ), the risk of cutaneous squamous cell carcinoma (cSCC) might be increased among patients with diabetes. This study aimed to estimate the risk of cSCC among HCTZ users with type 2 diabetes, and to determine whether thiazide-like diuretics, another drug in the same class with HCTZ, would be safer. Methods: We linked the benchmarking database in Dutch primary care, the Netherlands Cancer Registry, and the Dutch Personal Records Database (1998–2019). All 71,648 patients were included, except for those who had a history of skin cancer prior to cohort entry. We used Cox modeling to estimate the HRs and 95% confidence intervals for cSCC. The model was adjusted by cumulative exposure to each antihypertensive, age, sex, smoking, body mass index, blood pressure, serum creatinine, other confounding drug use at cohort entry, and cohort entry year. Results: There were 1,409 cSCC events (23 among thiazide-like diuretics users), during a follow-up of 679,789 person-years. Compared with no HCTZ use, the adjusted HRs for HCTZ use were 1.18 (1.00–1.40) for ≤2 years, 1.57 (1.32–1.88) for 2 to 4 years, and 2.09 (1.73–2.52) for >4 years. The HR was 0.90 (0.79–1.03) for an additional year of thiazide-like diuretic use. Conclusions: In patients with diabetes, exposure to HCTZ for >2 years is associated with an increased risk of cSCC, whereas no increased risk associated with thiazide-like diuretics was observed. Impact: The potential increased risk of cSCC should be a consideration when prescribing HCTZ, with thiazide-like diuretics offering a safer alternative.
Association of Elbow Flexor MRI Fat Fraction With Loss of Hand-to-Mouth Movement in Patients With Duchenne Muscular Dystrophy

Background and Objectives To study the potential of quantitative MRI (qMRI) fat fraction (FF) as a biomarker in nonambulant patients with Duchenne muscular dystrophy (DMD), we assessed the additive predictive value of elbow flexor FF to age at loss of hand-to-mouth movement. Methods Nonambulant patients with DMD (age ≥8 years) were included. Four-point Dixon MRI scans of the right upper arm were performed at baseline and at the 12-, 18-, or 24-month follow-up. Elbow flexor FFs were determined from 5 central slices. Loss of hand-to-mouth movement was determined at study visits and by phone calls every 4 months. FFs were fitted to a sigmoidal curve by use of a mixed model with random slope to predict individual trajectories. The added predictive value of elbow flexor FF to age at loss of hand-to-mouth movement was calculated from a Cox model with the predicted FF as a time-varying covariate, yielding a hazard ratio. Results Forty-eight MRIs of 20 patients with DMD were included. The hazard ratio of a percent-point increase in elbow flexor FF for the time to loss of hand-to-mouth movement was 1.12 (95% confidence interval 1.04–1.21; p = 0.002). This corresponded to a 3.13-fold increase in the instantaneous risk of loss of hand-to-mouth movement in patients with a 10–percent points higher elbow flexor FF at any age. Discussion In this prospective study, elbow flexor FF predicted loss of hand-to-mouth movement independently of age. qMRI-measured elbow flexor FF can be used as a surrogate endpoint or stratification tool for clinical trials in nonambulant patients with DMD. Classification of Evidence This study provides Class II evidence that qMRI FF of elbow flexor muscles in patients with DMD predicts loss of hand-to-mouth movement independently of age.