Miracle-dz/UniFAR-FTUs huggingface dataset:
The rice foot rot pathogen Dickeya zeae alters the in‐field plant microbiome

Summary Studies on bacterial plant diseases have thus far been focused on the single bacterial species causing the disease, with very little attention given to the many other microorganisms present in the microbiome. This study intends to use pathobiome analysis of the rice foot rot disease, caused by Dickeya zeae, as a case study to investigate the effects of this bacterial pathogen to the total resident microbiome and to highlight possible interactions between the pathogen and the members of the community involved in the disease process. The microbiome of asymptomatic and the pathobiome of foot‐rot symptomatic field‐grown rice plants over two growing periods and belonging to two rice cultivars were determined via 16S rRNA gene amplicon sequencing. Results showed that the presence of D. zeae is associated with an alteration of the resident bacterial community in terms of species composition, abundance and richness, leading to the formation of microbial consortia linked to the disease state. Several bacterial species were significantly co‐presented with the pathogen in the two growing periods suggesting that they could be involved in the disease process. Besides, culture‐dependent isolation and in planta inoculation studies of a bacterial member of the pathobiome, identified as positive correlated with the pathogen in our in silico analysis, indicated that it benefits from the presence of D. zeae. A similar microbiome/pathobiome experiment was also performed in a symptomatically different rice disease evidencing that not all plant diseases have the same consequence/relationship with the plant microbiome. This study moves away from a pathogen‐focused stance and goes towards a more ecological perception considering the effect of the entire microbial community which could be involved in the pathogenesis, persistence, transmission and evolution of plant pathogens.
Uncommon case of complete loss of hunger following an isolated left insular stroke

ABSTRACT The insula has long been among the least understood regions of the human brain, in part due to its restricted accessibility. Mounting evidence suggests that the insula is a prominent player in gustatory, interoceptive, and emotional processing, and likely integrates these different functions to contribute to the homeostatic control of food intake. Here we report the case of a young adult patient who lost the subjective experience of hunger following an ischemic stroke localized in the posterior left insula. The loss of hunger was not attributable to medication, substance use, or a clinical disorder, and lasted for a period of 15 months. In line with the role attributed to the insula in gustation and interoception, we suggest that the insula integrates information about taste, interoception, and the hedonic value of food in the service of homeostatic regulation.
Assembly of Covalently Inorganic-Organic Hybrid Molecular Framework Based on Porphyrin and Phthalocyanine Derivatives—Sensitizer for Dye Sensitized Solar Cells

The research on sensitizer for dye sensitized solar cells based on (metallo)porphyrin/phthalocyanine materials were reviewed, and experimental design and assembly method were advised. Latest progress and research status of sensitizer dyes based on metalloporphyrins applied in dye sensitized solar cells was summarized. The preparation and construction of sensitizer electrodes and dye sensitized solar cells based on metal organic frameworks (MOFs) of (metallo)porphyrin/phthalocyanine were projected.
Spinal lumbar dI2 interneurons contribute to stability of bipedal stepping

Peripheral and intraspinal feedback is required to shape and update the output of spinal networks that execute motor behavior. We report that lumbar dI2 spinal interneurons in chicks receive synaptic input from afferents and premotor neurons. These interneurons innervate contralateral premotor networks in the lumbar and brachial spinal cord, and their ascending projections innervate the cerebellum. These findings suggest that dI2 neurons function as interneurons in local lumbar circuits, are involved in lumbo-brachial coupling, and that part of them deliver peripheral and intraspinal feedback to the cerebellum. Silencing of dI2 neurons leads to destabilized stepping in posthatching day 8 hatchlings, with occasional collapses, variable step profiles, and a wide-base walking gait, suggesting that dI2 neurons may contribute to the stabilization of the bipedal gait.
Seeing the Invisible

Abstract A 76-year-old woman with uterine cervical cancer 20 years ago received right total hip replacement 3 months ago for right hip avascular necrosis without specific intraoperative finding. She reported persistent right hip pain after falling from bed. Pelvic x-ray showed right pubic ramus fracture. To evaluate prosthesis loosening, 99mTc-MDP 3-phase bone scan was arranged, showing diffusely and heterogeneously increased vascularity and tracer perfusion over the right hip, with intensely and heterogeneously increased metabolism in the right iliac bone and hip. SPECT/CT showed nearby swelling of calcified muscles. After debridement and synovectomy, the pathologic report showed chondroblastic osteosarcoma.
Land‐use change and biodiversity: Challenges for assembling evidence on the greatest threat to nature

Land‐use change is considered the greatest threat to nature, having caused worldwide declines in the abundance, diversity, and health of species and ecosystems. Despite increasing research on this global change driver, there are still challenges to forming an effective synthesis. The estimated impact of land‐use change on biodiversity can depend on location, research methods, and taxonomic focus, with recent global meta‐analyses reaching disparate conclusions. Here, we critically appraise this research body and our ability to reach a reliable consensus. We employ named entity recognition to analyze more than 4000 abstracts, alongside full reading of 100 randomly selected papers. We highlight the broad range of study designs and methodologies used; the most common being local space‐for‐time comparisons that classify land use in situ. Species metrics including abundance, distribution, and diversity were measured more frequently than complex responses such as demography, vital rates, and behavior. We identified taxonomic biases, with vertebrates well represented while detritivores were largely missing. Omitting this group may hinder our understanding of how land‐use change affects ecosystem feedback. Research was heavily biased toward temperate forested biomes in North America and Europe, with warmer regions being acutely underrepresented despite offering potential insights into the future effects of land‐use change under novel climates. Various land‐use histories were covered, although more research in understudied regions including Africa and the Middle East is required to capture regional differences in the form of current and historical land‐use practices. Failure to address these challenges will impede our global understanding of land‐use change impacts on biodiversity, limit the reliability of future projections and have repercussions for the conservation of threatened species. Beyond identifying literature biases, we highlight the research priorities and data gaps that need urgent attention and offer perspectives on how to move forward.
Weight misperception and its associations with eating disorder symptoms over the course of residential eating disorder treatment.

OBJECTIVE Although individuals with eating disorders (EDs) often experience significant body dissatisfaction and perceptual body image distortions, the presence and impact of weight misperception in clinical samples have been minimally examined. The aims of this study were to quantify weight misperception in individuals with EDs, examine whether weight misperception predicts ED severity at treatment discharge, and explore changes in weight misperception across treatment. METHOD Participants were 98 women seeking residential treatment for their ED who reported weekly on their perceived weight. Objectively measured weight was subtracted from perceived weight to determine weekly "weight misperception. " Participants completed the Eating Disorder Examination Questionnaire (EDE-Q) at intake and discharge to assess ED severity. Weight misperception at intake and change in weight misperception over treatment were examined as predictors of ED pathology at discharge. RESULTS Approximately 74.5% of the sample overestimated their weight, with an average weight misperception of 2.7 (SD = 5.6) pounds (1.2 kg; SD = 2.5). Weight misperception spanned from -6.2 to 43.6 pounds (-2.8 to 19.8 kg) and did not differ based on ED diagnosis. On average, weight misperception increased throughout treatment. Greater weight misperception at intake as well as greater increases in weight misperception over treatment significantly predicted EDE-Q scores at discharge. DISCUSSION Findings highlight that weight misperception is not limited to underweight patients. Misperceiving one's weight may predict symptom severity across a range of EDs, and future research is needed to examine whether targeting weight misperception during residential treatment could improve treatment outcomes for individuals with EDs.
p53 regulation by MDM2 contributes to self‐renewal and differentiation of basal stem cells in mouse and human airway epithelium

Proper physiological function of mammalian airways requires the differentiation of basal stem cells into secretory or multiciliated cells, among others. In addition, the self‐renewal ability of these basal stem cells is crucial for developing a quick response to toxic agents in order to re‐establish the epithelial barrier function of the airways. Although these epithelial missions are vital, little is known about those mechanism controlling airway epithelial regeneration in health and disease. p53 has been recently proposed as the guardian of homeostasis, promoting differentiation programs, and antagonizing a de‐differentiation program. Here, we exploit mouse and human tracheal epithelial cell culture models to study the role of MDM2‐p53 signaling in self‐renewal and differentiation in the airway epithelium. We show that p53 protein regulation by MDM2 is crucial for basal stem cell differentiation and to keep proper cell proliferation. Therefore, we suggest that MDM2/p53 interaction modulation is a potential target to control regeneration of the mammalian airway epithelia without massively affecting the epithelium integrity and differentiation potential.
A Specialized Nutritional Formulation Prevents Hippocampal Glial Activation and Memory Impairment Induced by Amyloid-β Oligomers in Mice.

BACKGROUND Alzheimer's disease (AD) is the most common cause of dementia in the elderly and is characterized by progressive cognitive decline. Considerable evidence supports an important role of amyloid-β oligomers (AβOs) in the pathogenesis of AD, including the induction of aberrant glial activation and memory impairment. OBJECTIVE We have investigated the protective actions of a nutritional formulation, denoted AZ formulation, on glial activation and memory deficits induced by intracerebroventricular (i.c.v.) infusion of AβOs in mice. METHODS Two-month-old male mice were treated orally with AZ formulation or isocaloric placebo for 30 consecutive days. Microglial and astrocytic activation were analyzed by immunohistochemistry in the hippocampus 10 days after i.c. v. infusion of AβOs (n = 5 mice per experimental condition). Memory loss was assessed by the novel object recognition (NOR) test (n = 6-10 mice per experimental condition). RESULTS Oral treatment with the AZ formulation prevented hippocampal microglial and astrocytic activation induced by i.c. v. infusion of AβOs. The AZ formulation further protected mice from AβO-induced memory impairment. CONCLUSION Results suggest that administration of the AZ formulation may comprise a promising preventative and non-pharmacological strategy to reduce brain inflammation and attenuate memory impairment in AD.
Phenotype Analysis and Genetic Study of Chinese Patients With Treacher Collins Syndrome

Objective The aim of this study was to confirm the pathogenic variants, explore the genotype–phenotype correlation and characteristics of Chinese patients with Treacher Collins syndrome (TCS). Design Clinical details of 3 TCS family cases and 2 sporadic cases were collected and analyzed. Whole-exome sequencing and Sanger sequencing were conducted to detect causative variants. Setting Tertiary clinical care. Patients This study included 8 patients clinically diagnosed with TCS who were from 3 familial cases and 2 sporadic cases. Main Outcome Measures When filtering the database, variants were saved as rare variants if their frequency were less than 0.005 in the 1000 Genomes Project Database, the Exome Aggregation Consortium (ExAC) browser, and the Novogene database, or they would be removed as common ones. The pathogenic variants identified were verified by polymerase chain reaction. The sequencing results were analyzed by Chromas 2.1 software. Results Two novel pathogenic variants (NM_000356.3: c.537del and NM_000356.3: c.1965_1966dupGG) and 2 known pathogenic variants (NM_000356.3: c.1535del, NM_000356.3: c.4131_4135del) were identified within TCOF1 which are predicted to lead to premature termination codons resulting in a truncated protein. There was a known missense SNP (NM_015972.3: c.139G>A) within POLR1D. No phenotype–genotype correlation was observed. Instead, these 8 patients demonstrated the high genotypic and phenotypic heterogeneity of TCS. Conclusions This study expands on the pathogenic gene pool of Chinese patients with TCS. Besides the great variation among patients which is similar to international reports, Chinese patients have their own characteristics in clinical phenotype and pathogenesis mutations.
Host Genetic Risk Factors for Chlamydia trachomatis-Related Infertility in Women.

BACKGROUND Chlamydia trachomatis (Ct) infection ascending to the upper genital tract can cause infertility. Direct association of genetic variants as contributors is challenging because infertility may not be diagnosed until years after infection. Investigating the intermediate trait of ascension bridges this gap. METHODS We identified infertility genome-wide association study (GWAS) loci using deoxyribonucleic acid from Ct-seropositive cisgender women in a tubal factor infertility study and Ct-infected cisgender women from a longitudinal pelvic inflammatory disease cohort with known fertility status. Deoxyribonucleic acid and blood messenger ribonucleic acid from 2 additional female cohorts with active Ct infection and known endometrial infection status were used to investigate the impact of infertility single-nucleotide polymorphisms (SNPs) on Ct ascension. A statistical mediation test examined whether multiple infertility SNPs jointly influenced ascension risk by modulating expression of mediator genes. RESULTS We identified 112 candidate infertility GWAS loci, and 31 associated with Ct ascension. The SNPs altered chlamydial ascension by modulating expression of 40 mediator genes. Mediator genes identified are involved in innate immune responses including type I interferon production, T-cell function, fibrosis, female reproductive tract health, and protein synthesis and degradation. CONCLUSIONS We identified Ct-related infertility loci and their potential functional effects on Ct ascension.
The prognostic significance of the lipid profile after an ischemic stroke

ABSTRACT Background The role that cholesterol levels play in stroke is still uncertain, especially in secondary prevention. The aim was to determine how a comprehensive analysis of the lipid profile can be associated with post-stroke outcomes. Consecutive patients diagnosed with ischemic stroke were included in our cohort and followed up for 24months. Baseline clinical and demographic data were collected as well as a complete lipid profile 6-months after the index stroke. Lipid variables were analyzed quantitatively and qualitatively. Clinical outcomes included stroke recurrence, major cardiovascular events, and functional performance (assessed with the modified Rankin scale). Results The study included 588 patients with an average age of 58.3 years. There were 148 (25.2%) patients with high total cholesterol, 260 (44.2%) with low HDL, 180 (30.6%) with high LDL, and 204 (34.7%) with high triglycerides. There were 164 (27.9%) patients with no abnormalities in the lipid profile. After the follow-up, 108 (18.3%) had another stroke, 32 (5.4%) had major cardiovascular events, and 360 (61.2%) presented good functional outcomes. A higher LDL-C/HDL-C ratio and a low HDL-C level were significantly associated with worse cardiovascular outcomes. The detection of LDL-C > 70 mg/dL was an independent predictor of a higher risk of stroke recurrence and worse functional performance. The greater the number of altered lipid variables, the greater the chance of developing an unfavorable composite outcome and presenting cardiovascular events after the stroke. Conclusions The complete analysis of the lipid panel allows the determination of the prognosis of patients who suffered a stroke.
Treatment Escalation vs Immediate Initiation of Highly Effective Treatment for Patients With Relapsing-Remitting Multiple Sclerosis: Data From 2 Different National Strategies.

Importance Treatment strategies for relapsing-remitting multiple sclerosis (RRMS) vary markedly between Denmark and Sweden. The difference in the association of these national strategies with clinical outcomes is unknown. Objective To investigate the association of national differences in disease-modifying treatment (DMT) strategies for RRMS with disability outcomes. Design, Setting, and Participants This cohort study used data on 4861 patients from the Danish and Swedish national multiple sclerosis (MS) registries from the date of index DMT initiation (between January 1, 2013, and December 31, 2016) until the last recorded visit at time of data extraction (October 2, 2019). Exposures All MS-specific DMTs initiated during the observation period were included in the analysis. Main Outcomes and Measures The primary study outcome was time to 24-week confirmed disability worsening. Secondary outcomes were 24-week confirmed disability improvement, milestone Expanded Disability Status Scale scores of 3 and 4, annualized relapse rate, time to first relapse, and treatment switching. Data were analyzed using inverse probability of treatment weighting-based models using a propensity score to weight and correct the comparison for the imbalance of confounders observed at baseline between the 2 countries. Results A total of 2700 patients from the Swedish MS registry (1867 women [69.2%]; mean [SD] age, 36.1 [9.5] years) and 2161 patients from the Danish MS registry (1472 women [68.1%]; mean [SD] age, 37.3 [9.4 years]) started a first DMT between 2013 and 2016, were included in the analysis, and were observed for a mean (SD) of 4.1 (1.5) years. A total of 1994 Danish patients (92.3%) initiated a low to moderately effective DMT (teriflunomide, 907 [42.0%]) and 165 (7.6%) initiated a highly effective DMT, whereas a total of 1769 Swedish patients (65.5%) initiated a low to moderately effective DMT (teriflunomide, 64 [2.4%]) and 931 (34.5%) initiated a highly effective DMT. The Swedish treatment strategy was associated with a 29% reduction in the rate of postbaseline 24-week confirmed disability worsening relative to the Danish treatment strategy (hazard ratio, 0.71; 95% CI, 0.57-0.90; P = .004). The Swedish treatment strategy was also associated with a 24% reduction in the rate of reaching an expanded disability status scale score of 3 (hazard ratio, 0.76; 95% CI, 0.60-0.97; P = .03) and a 25% reduction in the rate of reaching an expanded disability status scale score of 4 (hazard ratio, 0.75; 95% CI, 0.61-0.96; P = .01) relative to Danish patients. Conclusions and Relevance The findings of this study suggest that there is an association between differences in treatment strategies for RRMS and disability outcomes at a national level. Escalation of treatment efficacy was inferior to using more efficacious DMT as initial treatment.
Control System Design of Power Tracking for PEM Fuel Cell Automotive Application

Owing to load variations, the power tracking of fuel cells in automotive applications is emphasized. We address the control strategies to meet varying power demands while optimizing system efficiency. Based on the control‐oriented proton exchange membrane fuel cell model, the relative gain array is analyzed to determine variable parings in control design. As the dynamics of two control variables are different, a cascade control architecture is adopted. A feedforward‐feedback composite control is used to achieve fast response and eliminate the stable error. To avoid oxygen starvation at power transients, an oxygen excess ratio constrained strategy is proposed to limit the load current if there is lack of reaction oxygen. A mixed‐sensitivity synthesis is applied to suppress parameter perturbation and improve system robustness. To further suppress the fluctuations of the oxygen excess ratio and achieve the maximum system efficiency, an oxygen excess ratio invariant strategy is developed, which coordinates load current with airflow. A comparative study is conducted, with two scenarios of power tracking and fuel cell degradation. The results show that the mixed‐sensitivity strategy has a fast response in power tracking and effective perturbation suppression performance, while the oxygen excess ratio invariant strategy maximizes the system efficiency.
Ways & Means Rational Protein Crystallization by Mutational Surface Engineering

Summary the range of conditions. As the proverbial “low-hanging fruit,”i.e.,easilycrystallizedsmall-tomedium-sizedpro- Protein crystallization constitutes a limiting step in teins, falls prey to high-throughput efforts, the “high-structure determination by X-ray diffraction. Even if hanging fruit” presents an increasing challenge. singlecrystalsareavailable,inadequatephysicalqual- One of the ways to address the problem of efficient ity may seriously limit the resolution of the available crystallization is homolog screening, pioneered over 50 data and consequently the accuracy of the atomic years ago (Campbell et al., 1972; Kendrew et al., 1954). model. Recent studies show that targeted mutagene- The concept is simple: if you cannot grow crystals of the sis of surface patches containing residues with large protein you want, try growing crystals of a homologous flexible sidechains and their replacementwith smaller protein with a similar or identical function. This ap- aminoacidsleadtoeffectivepreparationofX-rayqual-
The search for the meaning of life in soil: an opinion

The introduction of impressive technologies in the search for life's diversity and activity in soil has led to remarkable new techniques and knowledge concerning the soil microbial community. These have led to finding some important links to function. However, we attest that the general lack of causality found between the many metrics of microbial diversity and populations of soil microbes and function is due, at least in part, to the lack of understanding of the links between microbial populations and dynamics to their physical habitat and attendant moisture conditions. In this opinion paper we explore the importance of this interplay between organism and habitat. Further, as an example of this interplay, we introduce the potential importance of nematode movement and gene transfer in bacterial populations.