Miracle-dz/UniFAR-FTUs huggingface dataset:
Unbiased in vivo preclinical evaluation of anticancer drugs identifies effective therapy for the treatment of pancreatic adenocarcinoma

Significance The clinical management of pancreatic cancer has not seen significant improvement in decades, in part because prediction of tumor drug sensitivity using in vitro assays has proven notoriously inaccurate in this disease. We performed a large-scale, unbiased in vivo screen of 57 different single agent and combination targeted therapies in an in vivo orthotopic mouse model. In this ambitious effort, we identified previously unsuspected synergy between HSP90 inhibition and MEK inhibition as effective combination therapy in this disease. The results underscore the utility of unbiased, in vivo drug screens in the identification of effective cancer therapies for evaluation in subsequent clinical trials. Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at an advanced stage, which limits surgical options and portends a dismal prognosis. Current oncologic PDAC therapies confer marginal benefit and, thus, a significant unmet clinical need exists for new therapeutic strategies. To identify effective PDAC therapies, we leveraged a syngeneic orthotopic PDAC transplant mouse model to perform a large-scale, in vivo screen of 16 single-agent and 41 two-drug targeted therapy combinations in mice. Among 57 drug conditions screened, combined inhibition of heat shock protein (Hsp)-90 and MEK was found to produce robust suppression of tumor growth, leading to an 80% increase in the survival of PDAC-bearing mice with no significant toxicity. Mechanistically, we observed that single-agent MEK inhibition led to compensatory activation of resistance pathways, including components of the PI3K/AKT/mTOR signaling axis, which was overcome with the addition of HSP90 inhibition. The combination of HSP90(i) + MEK(i) was also active in vitro in established human PDAC cell lines and in vivo in patient-derived organoid PDAC transplant models. These findings encourage the clinical development of HSP90(i) + MEK(i) combination therapy and highlight the power of clinically relevant in vivo model systems for identifying cancer therapies.
The 1B vaccine strain of Chlamydia abortus produces placental pathology indistinguishable from a wild type infection

Chlamydia abortus is one of the most commonly diagnosed causes of infectious abortion in small ruminants worldwide. Control of the disease (Enzootic Abortion of Ewes or EAE) is achieved using the commercial live, attenuated C. abortus 1B vaccine strain, which can be distinguished from virulent wild-type (wt) strains by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Published studies applying this typing method and whole-genome sequence analyses to cases of EAE in vaccinated and non-vaccinated animals have provided strong evidence that the 1B strain is not attenuated and can infect the placenta causing disease in some ewes. Therefore, the objective of this study was to characterise the lesions found in the placentas of ewes vaccinated with the 1B strain and to compare these to those resulting from a wt infection. A C. abortus-free flock of multiparous adult ewes was vaccinated twice, over three breeding seasons, each before mating, with the commercial C. abortus 1B vaccine strain (Cevac® Chlamydia, Ceva Animal Health Ltd.). In the second lambing season following vaccination, placentas (n = 117) were collected at parturition and analysed by C. abortus-specific real-time quantitative PCR (qPCR). Two placentas, from a single ewe, which gave birth to live twin lambs, were found to be positive by qPCR and viable organisms were recovered and identified as vaccine type (vt) by PCR-RFLP, with no evidence of any wt strain being present. All cotyledons from the vt-infected placentas were analysed by histopathology and immunohistochemistry and compared to those from wt-infected placentas. Both vt-infected placentas showed lesions typical of those found in a wt infection in terms of their severity, distribution, and associated intensity of antigen labelling. These results conclusively demonstrate that the 1B strain can infect the placenta, producing typical EAE placental lesions that are indistinguishable from those found in wt infected animals.
Al-Tolerant Barley Mutant hvatr.g Shows the ATR-Regulated DNA Damage Response to Maleic Acid Hydrazide

ATR, a DNA damage signaling kinase, is required for cell cycle checkpoint regulation and detecting DNA damage caused by genotoxic factors including Al3+ ions. We analyzed the function of the HvATR gene in response to chemical clastogen-maleic acid hydrazide (MH). For this purpose, the Al-tolerant barley TILLING mutant hvatr.g was used. We described the effects of MH on the nuclear genome of hvatr.g mutant and its WT parent cv. “Sebastian”, showing that the genotoxic effect measured by TUNEL test and frequency of cells with micronuclei was much stronger in hvatr.g than in WT. MH caused a significant decrease in the mitotic activity of root cells in both genotypes, however this effect was significantly stronger in “Sebastian”. The impact of MH on the roots cell cycle, analyzed using flow cytometry, showed no differences between the mutant and WT.
MoSec61β, the beta subunit of Sec61, is involved in fungal development and pathogenicity, plant immunity, and ER-phagy in Magnaporthe oryzae

ABSTRACT The process of protein translocation into the endoplasmic reticulum (ER) is the initial and decisive step in the biosynthesis of all secretory proteins and many soluble organelle proteins. In this process, the Sec61 complex is the protein-conducting channel for transport. In this study, we identified and characterized the β subunit of the Sec61 complex in Magnaporthe oryzae (MoSec61β). Compared with the wild-type strain Guy11, the ΔMosec61β mutant exhibited highly branched mycelial morphology, reduced conidiation, high sensitivity to cell wall integrity stress, severely reduced virulence to rice and barley, and restricted biotrophic invasion. The turgor pressure of ΔMosec61β was notably reduced, which affected the function of appressoria. Moreover, ΔMosec61β was also sensitive to oxidative stress and exhibited a reduced ability to overcome plant immunity. Further examination demonstrated that MoSec61β affected the normal secretion of the apoplastic effectors Bas4 and Slp1. In addition, ΔMosec61β upregulated the level of ER-phagy. In conclusion, our results demonstrate the importance of the roles played by MoSec61β in the fungal development and pathogenesis of M. oryzae.
Integrating carbon emission, accumulation and transport in inland waters to understand their role in the global carbon cycle

Inland waters receive a significant quantity of carbon (C) from land. The fate of this C during transit, whether it is emitted to the atmosphere, accumulated in sediments or transported to the ocean, can considerably reshape the landscape C balance. However, these different fates of terrestrial C are not independent but are instead linked via several catchment and aquatic processes. Thus, according to mass conservation, any environmental change inducing a shift in a particular C fate should come at the expense of at least one other fate. Nonetheless, studies that have investigated C emission, accumulation and transport concertedly are scarce, resulting in fragmented knowledge of the role of inland waters in the global C cycle. Here, we propose a framework to understand how different C fates in aquatic systems are interlinked and covary under environmental changes. First, to explore how C fates are currently distributed in streams, rivers, reservoirs and lakes, we compiled data from the literature and show that ‘C fate allocation’ varies widely both within and among inland water systems types. Secondly, we developed a framework that integrates C fates in any inland water system by identifying the key processes underlying their linkages. Our framework places the partitioning between the different C forms, and how this is controlled by export from land, internal transformations and hydrology, as central to understanding C fate allocation. We argue that, by focusing on a single fate, studies could risk drawing misleading conclusions regarding how environmental changes will alter the role of inland waters in the global C cycle. Our framework thus allows us to holistically assess the consequences of such changes on coupled C fluxes, setting a foundation for understanding the contemporary and future fate of land‐derived C in inland water systems.
Healthcare Utilization Following Traumatic Brain Injury in a Large National Sample.

OBJECTIVE To evaluate the impact of traumatic brain injury (TBI) on healthcare utilization (HCU) over a 1-year period in a large national sample of individuals diagnosed with TBI across multiple care settings. SETTING Commercial insurance enrollees. PARTICIPANTS Individuals with and without TBI, 2008-2014. DESIGN Retrospective cohort. MAIN MEASURES We compared the change in the 12-month sum of inpatient, outpatient, emergency department (ED), and prescription HCU from pre-TBI to post-TBI to the same change among a non-TBI control group. Most rehabilitation visits were not included. We stratified models by age ≥65 and included the month of TBI in subanalysis. RESULTS There were 207 354 individuals in the TBI cohort and 414 708 individuals in the non-TBI cohort. Excluding the month of TBI diagnosis, TBI resulted in a slight increase in outpatient visits (rate ratio [RtR] = 1.05; 95% confidence interval [CI], 1.04-1.06) but decrease in inpatient HCU (RtR = 0.86; 95% CI, 0.84-0.88). Including the month of TBI in the models resulted in increased inpatient (RtR = 1.55; 95% CI, 1.52-1.58) and ED HCU (RtR = 1.37; 95% CI, 1.34-1.40). CONCLUSION In this population of individuals who maintained insurance coverage following TBI, results suggest that TBI may have a limited impact on nonrehabilitation HCU at the population level.
Integrity of the post-LRR domain is required for TNLs' function.

Plants trigger appropriate defense responses notably through intracellular nucleotide-binding (NB) and leucine-rich repeat (LRR) containing receptor genes (NLRs) that detect secreted pathogen effector proteins. In NLR resistance genes, the toll/interleukin-1 receptor (TIR)-NB-LRRs (TNLs) are an important subfamily out of which approximately half members carry a post-LRR (PL) domain of unknown role. We first investigated the requirement of the PL domain for TNL-mediated immune response by mutating the most conserved amino acids across PL domains of Arabidopsis thaliana TNLs. We identified several amino acids in the PL domain of RPS4 required for its ability to trigger a hypersensitive response to AvrRps4 in N. tabacum transient assay. Mutating the corresponding amino acids within the PL domain of the tobacco TNL gene N also affected its function. Consequently, our results indicate that the integrity of the PL domain at conserved positions is crucial for at least two unrelated TNLs. We then tested the PL domain specificity for function by swapping PL domains between the paralogs RPS4 and RPS4B. Our results suggest that the PL domain is involved in their TNL pair specificity, 'off state' stability and NLR complex activation. Considering genetically paired Arabidopsis TNLs, we finally compared the PL and TIR domains of their sensor and executor sequences, respectively. While TIR and PL domains from executors present complete motifs, sensors showed a lack of conservation with degenerated motifs. We provide here a first contribution to the functional analysis of the PL domain in order to decipher its role for TNLs' function.
Severe Hypoglycemia, Cardiac Structure and Function, and Risk of Cardiovascular Events Among Older Adults With Diabetes.

OBJECTIVE To assess the association of severe hypoglycemia measured at baseline with cardiovascular disease (CVD) among community-dwelling older individuals with diabetes, a group particularly susceptible to hypoglycemia. RESEARCH DESIGN AND METHODS We included older adults with diabetes from the Atherosclerosis Risk in Communities (ARIC) study who attended visit 5 (2011-2013, baseline). Severe hypoglycemia at baseline was defined with use of first position ICD-9 codes from hospitalizations, emergency department visits, and ambulance calls. We examined cross-sectional associations of severe hypoglycemia with echocardiographic indices of cardiac structure-function. We prospectively evaluated the risks of incident or recurrent CVD (coronary heart disease, stroke, or heart failure) and all-cause mortality, from baseline to 31 December 2018, using negative binomial and Cox regression models. RESULTS Among 2,193 participants (mean [SD] age 76 [5] years, 57% female, 32% blacks), 79 had a history of severe hypoglycemia at baseline. Severe hypoglycemia was associated with a lower left ventricular (LV) ejection fraction (adjusted β-coefficient -3.66% [95% CI -5.54, -1.78]), higher LV end diastolic volume (14.80 mL [95% CI 8.77, 20.84]), higher E-to-A ratio (0.11 [95% CI 0.03, 0.18]), and higher septal E/e' (2.48 [95% CI 1.13, 3.82]). In adjusted models, severe hypoglycemia was associated with incident or recurrent CVD (incidence rate ratio 2.19 (95% CI 1.24, 3.88]) and all-cause mortality (hazard ratio 1.71 [95% CI 1.10, 2.67]) among those without prevalent CVD. CONCLUSIONS Our findings suggest that a history of severe hypoglycemia is associated with alterations in cardiac function and is an important marker of future cardiovascular risk in older adults.
Comparison of In Vivo and In Vitro Digestibility in Donkeys

Simple Summary Traditional in vivo methods of determining digestibility of feeds are expensive and time-consuming, and very few data are available for donkeys. The aim of this study was to verify if the in vitro method developed for the Ankom DaisyII Incubator could produce accurate estimates of the in vivo dry matter and neutral detergent fiber digestibility of diets fed to donkeys. Four donkeys and four diets were used in the trial, and the experiment was repeated four times. Buffered donkey feces were used as an inoculum source for the assessment of digestibility in vitro, with an incubation time of 60 h. The obtained results showed that the Ankom DaisyII Incubator ranked the diets in the same order as the in vivo method. However, in vitro values were lower than those obtained in vivo. The regression analyses used to predict in vivo estimates from in vitro data gave poor results and low precision. In conclusion, further studies, using different sample size and digestion times in vitro, are needed to verify if accurate prediction of in vivo feed digestibility can be obtained using the Ankom DaisyII Incubator and donkey feces as inoculum. Abstract We compared in vivo and in vitro dry matter (DM) and neutral detergent fiber (NDF) digestibility in donkeys using feces as microbial inoculum. Four donkeys were used in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments. The animals were fed two types of hay, with or without flaked barley. For the in vivo procedure, total feces were collected for 6 days from each donkey; digestibility was calculated as the difference between ingested and excreted DM and NDF. For the in vitro procedure, donkey feces were buffered and used as microbial inoculum in an Ankom DaisyII Incubator; digestibility was estimated after 60 h of incubation. In vivo results showed that the addition of barley to hays did not change the digestibility values. In vivo estimates were higher than in vitro ones. The equations used to predict in vivo estimates from in vitro data were not reliable (R2 = 0.47 and 0.21; P = 0.003 and 0.078 for NDF and DM digestibility, respectively). Further studies need to evaluate different sample size and digestion times.
Changing patterns of thalassaemia in Italy: a WebThal perspective.

BACKGROUND Migration has impacted the spread of thalassaemia which is gradually becoming a global health problem. Italy, with an approximate estimation of 7,000 patients, does not have an accurate national record for haemoglobinopathies. This cross-sectional evaluation includes data for approximately 50% of beta-thalassaemia patients in Italy to provide an overview of the burden of thalassaemia syndromes. MATERIAL AND METHODS The analysis included data on epidemiology, transfusions and clinical parameters from 3,986 thalassaemia patients treated at 36 centres in Italy who were alive on 31st December 2017. The study used WebThal, a computerised clinical record that is completely free-of-charge and that does not have any mandatory fields to be filled. RESULTS For patients with thalassaemia major, 68% were aged ≥35 years and 11% were aged ≤18 years. Patients with thalassaemia intermedia were slightly older. Transfusion data, reported in a subgroup of 1,162 patients, showed 9% had pre-transfusion haemoglobin <9 g/dL, 63% had levels between ≥9 and <10 g/dL, and 28% had levels ≥10 g/dL. These 1,162 patients underwent 22,272 transfusion days during 2017, with a mean of 19 transfusion days/year/patient (range 1-54 days). Severity of iron overload was reported in 756 patients; many had moderate or mild liver iron load (74% had liver iron <7.5 mg/g dry weight). In the same cohort, 85% of patients had no signs of cardiac iron load (MRT2* >20 ms), and only 3% showed signs of high-risk heart condition (T2* <10 ms). Most patients had normal alanine amino transferase levels due to treatment with the new anti-hepatitis C virus (HCV) drugs. DISCUSSION This study provides an overview of the current health status of patients with thalassaemia in Italy. Moreover, these data support the need for a national comprehensive thalassaemia registry.
Iron Therapy in Inflammatory Bowel Disease

The most common complication seen in inflammatory bowel disease (IBD) patients is iron deficiency anaemia (IDA). Symptoms such as chronic fatigue can be as debilitating to IBD patients as pathological symptoms of abdominal pain and diarrhoea. Recognising and correcting anaemia may be as important as managing IBD symptoms and improving overall quality of life. Thus, iron replacement should be commenced the moment IDA is identified. Although intravenous iron is now considered standard treatment for IBD patients in Europe, oral iron still appears to be the preferred option. Advantages of oral iron include greater availability, lower costs and ease of applicability. However, its multitude of side effects, impact on the microbiome and further exacerbating IBD activity can have consequences on patient compliance. The newer oral iron formulations show promising safety and efficacy data with a good side effect profile. Intravenous iron formulations bypass the gastrointestinal tract absorption thereby leading to less side effects. Multiple studies have shown its superiority compared to oral formulations although its risk for hypersensitivity reactions continue to lead to clinician hesitancy in prescribing this formulation. This article provides an updated review on diagnosis and management of IDA in IBD patients, discussing the newer oral and intravenous formulations.
Fracture of Thin-Walled Polyoxymethylene Bulk Specimens in Modes I and III

Thin-walled polymeric components are used in many applications. Hence, knowledge about their fracture behavior in bulk is beneficial in practice. Within this study, the double cantilever beam (DCB) and out-of-plane double cantilever beam (ODCB) tests are enhanced to enable the testing of such bulk specimens in mode I and mode III on the basis of the J-integral. This paper then presents and discusses the experimental results following the investigation of a semicrystalline polymer (polyoxymethylen) under quasi-static load conditions. From the experiments, fracture energies of similar magnitude in both mode I and mode III were determined. In mode III, pop-in fracture was observed. Furthermore, the fracture surfaces were investigated regarding the mode I and mode III dominant crack growth mechanisms, based on the morphology of the tested material. For specimens tested in mode I, no signs of plastic deformation were observed, and the fracture surface appears flat. In mode III, some samples display a twisted fracture surface (twisting angle close to 45°), which indicates local mode I crack growth. A transfer of the presented methodology to other (more ductile) polymeric materials is deemed possible without further restrictions. In addition, the presented setup potentially enables an investigation of polymeric bulk specimens in mixed mode I+III.
ICEHpsaHPS7, a Novel Multiple Drug Resistance Integrative Conjugative Element in Glaesserella parasuis

Integrative conjugative elements (ICEs) are a kind of novel self-transmissible mobile genetic element. In this study, a novel ICE was identified in Glaesserella (Haemophilus) parasuis. ABSTRACT Integrative conjugative elements (ICEs) are a kind of novel self-transmissible mobile genetic element. In this study, a novel ICE was identified in Glaesserella (Haemophilus) parasuis. We confirmed that it could mediate the migration of antimicrobial resistance genes in G. parasuis and found that there may have been a transferring potential between different serovar strains of G. parasuis. These findings demonstrate that the ICE is crucial to the horizontal transfer of antimicrobial resistance among G. parasuis strains.
Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR

Simple Summary Cells, life’s smallest units, are defined within the enclosure of thin, continuous membranes, which confine the molecular machinery required for the life and replication of cells. Crucially, membranes of cells establish and actively maintain distinctly different environments inside cells, including electrical and solute gradients vital to normal cellular functions. Membrane proteins are in charge of transport, electrical polarisation, signalling, membrane remodelling and other important functions. As such, membrane proteins are key drug targets and understanding their structure and function is essential to drug development and cellular control. Membrane proteins have physical characteristics that make such studies very challenging. Nuclear magnetic resonance is one advanced tool that enables structural studies of membrane proteins and their interactions at the atomic level of detail. We discuss the applications of NMR in solution and solid state to membrane protein studies alongside new developments in signal and sensitivity enhancement through dynamic nuclear polarisation. Abstract Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.