Miracle-dz/UniFAR-FTUs huggingface dataset:
The decomposition of organic matter in soils by fungi

Macromolecular structures, such as lignin and cellulose, are important components ofsoil organic carbon, the major terrestrial global carbon pool. The degradation of thesemacromolecules, including lignin and cellulose, in plant-derived soil organic matter, isimportant to the global carbon cycle. In grasslands, saprotrophic (decomposer) fungi aremajor decomposers of such organic material.Some of these compounds, such as lignin are relatively resistant to decay by themicrobial community if compared with other compound classes such as cellulose.In this work we investigate the involvement of fungi in the decomposition of both ligninand cellulose and look to link the decomposition processes observed in the field to thoseobserved in a laboratory-controlled environment.The key findings of this work are:-Field based experiments in both tropical and temperate environments indicatedthat lignin can be degraded completely, most likely by white-rot fungi, as shownby the shifts in the [Ac/Al]S, [Ac/Al]G and [S/G] relative lignin decompositionstate proxies. The results confirm that even in a very low carbon environment,fungi are able to completely degrade lignin over time. However, lignin isdegraded much faster in tropical environments. -Culturing experiments showed that it was possible to isolate a number of fungipresent on the degraded wheat straw collected in the field. , especially soft-rotfungi . When used in microcosm experiments using a range of organic substrates,the relative lignin decomposition state proxies indicated that Absidiacylindrospora and Trichoderma koningii are not able to completely degradelignin but preferentially degrade cellulose. -Cellulose degradation rates are much higher than those of lignin in degradedfield samples over time, confirming previous work.
A complication risk score to evaluate clinical severity of thalassaemia syndromes

The thalassaemia syndromes (TS) show different phenotype severity. Developing a reliable, practical and global tool to determine disease severity and tailor treatment would be of great value. Overall, 7910 patients were analysed with the aim of constructing a complication risk score (CoRS) to evaluate the probability of developing one or more complications. Nine independent variables were included in the investigation as predictors. Logistic regression models were used for Group A [transfusion‐dependent thalassaemia (TDT)], Group B [transfused non‐TDT (NTDT)] and Group C (non‐transfused NTDT). Statistically significant predictors included age (years), haemoglobin levels, hepatic transaminases [alanine aminotransferase (ALT) and aspartate aminotransferase] and left‐ventricular ejection fraction (LVEF) for Group A; age (years), age at first chelation (months), ALT and LVEF for Group B; and age (years), mean serum ferritin (SF) levels and LVEF for Group C. The area under the receiver operating characteristic curve was 84·5%, 82·1% and 80·0% for Groups A, Group B and Group C respectively, suggesting the models had good discrimination. Finally, the CoRS for each group was categorised into four risk classes (low, intermediate, high, and very high) using the centiles of its distribution. In conclusion, we have developed a CoRS for TS that can assist physicians in prospectively tailoring patients’ treatment.
Target-Centered Drug Repurposing Predictions of Human Angiotensin-Converting Enzyme 2 (ACE2) and Transmembrane Protease Serine Subtype 2 (TMPRSS2) Interacting Approved Drugs for Coronavirus Disease 2019 (COVID-19) Treatment through a Drug-Target Interaction Deep Learning Model

Previously, our group predicted commercially available Food and Drug Administration (FDA) approved drugs that can inhibit each step of the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using a deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI). Unfortunately, additional clinically significant treatment options since the approval of remdesivir are scarce. To overcome the current coronavirus disease 2019 (COVID-19) more efficiently, a treatment strategy that controls not only SARS-CoV-2 replication but also the host entry step should be considered. In this study, we used MT-DTI to predict FDA approved drugs that may have strong affinities for the angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane protease serine 2 (TMPRSS2) which are essential for viral entry to the host cell. Of the 460 drugs with Kd of less than 100 nM for the ACE2 receptor, 17 drugs overlapped with drugs that inhibit the interaction of ACE2 and SARS-CoV-2 spike reported in the NCATS OpenData portal. Among them, enalaprilat, an ACE inhibitor, showed a Kd value of 1.5 nM against the ACE2. Furthermore, three of the top 30 drugs with strong affinity prediction for the TMPRSS2 are anti-hepatitis C virus (HCV) drugs, including ombitasvir, daclatasvir, and paritaprevir. Notably, of the top 30 drugs, AT1R blocker eprosartan and neuropsychiatric drug lisuride showed similar gene expression profiles to potential TMPRSS2 inhibitors. Collectively, we suggest that drugs predicted to have strong inhibitory potencies to ACE2 and TMPRSS2 through the DTI model should be considered as potential drug repurposing candidates for COVID-19.
Memory Effect in the Spatial Series Based on Diamond and Graphite Crystals

To study the relation between the structure of a compound and its properties is one of the fundamental trends in chemistry and materials science. A classic example is the well-known influence of the structures of diamond and graphite on their physicochemical properties, in particular, hardness. However, some other properties of these allotropic modifications of carbon, e.g., fractal properties, are poorly understood. In this work, the spatial series (interatomic distance histograms) calculated using the crystal structures of diamond and graphite are investigated. Hurst exponents H are estimated using detrended fluctuation analysis and power spectral density. The values of H are found to be 0.27–0.32 and 0.37–0.42 for diamond and graphite, respectively. The calculated data suggest that the spatial series have long memory with a negative correlation between the terms of the series; that is, they are antipersistent.
Sensor Architectures and Technologies for Upper Limb 3D Surface Reconstruction: A Review

3D digital models of the upper limb anatomy represent the starting point for the design process of bespoke devices, such as orthoses and prostheses, which can be modeled on the actual patient’s anatomy by using CAD (Computer Aided Design) tools. The ongoing research on optical scanning methodologies has allowed the development of technologies that allow the surface reconstruction of the upper limb anatomy through procedures characterized by minimum discomfort for the patient. However, the 3D optical scanning of upper limbs is a complex task that requires solving problematic aspects, such as the difficulty of keeping the hand in a stable position and the presence of artefacts due to involuntary movements. Scientific literature, indeed, investigated different approaches in this regard by either integrating commercial devices, to create customized sensor architectures, or by developing innovative 3D acquisition techniques. The present work is aimed at presenting an overview of the state of the art of optical technologies and sensor architectures for the surface acquisition of upper limb anatomies. The review analyzes the working principles at the basis of existing devices and proposes a categorization of the approaches based on handling, pre/post-processing effort, and potentialities in real-time scanning. An in-depth analysis of strengths and weaknesses of the approaches proposed by the research community is also provided to give valuable support in selecting the most appropriate solution for the specific application to be addressed.
Increase in drugs-of-abuse findings in post-mortem toxicology due to COVID-19 restrictions - first observations in Finland.

A lot has been published on the anticipated effects of the current COVID-19 pandemic on users of illegal drugs. In this study we present evidence-based data on such effects, namely the increased number of drug findings in post-mortem investigations. All post-mortem toxicology cases positive for at least one of the following: buprenorphine, amphetamine, or cannabis, were investigated in the first 8 months of the year 2020 and the monthly numbers were compared to those in the previous 5 years from 2015-2019. These substances served as indicator analytes that could reveal changes in the drug using population. Right after the government restrictions came into force in March 2020, the numbers of buprenorphine, amphetamine and cannabis findings increased. The increase was most noticeable for amphetamine and was evident in all age groups. Our findings indicate that the assumptions on the increased risk of drug-related harm (including death) have become reality. Reduced access to harm-reduction services seems to have increased the mortality among individuals that use buprenorphine, amphetamine, or cannabis. Significant and prompt actions need to be taken in order to find new ways in helping this vulnerable group of people.
Assessing the effect of pregnancy intention at conception on the continuum of care in maternal healthcare services use in Bangladesh: Evidence from a nationally representative cross-sectional survey

Background The Continuum of Care (CoC; defined as accessing the recommended healthcare services during pregnancy and the early postpartum period) is low in lower-middle-income countries (LMICs). This may be a major contributor to the high rates of pregnancy-related complications and deaths in LMICs, particularly among women who had an unintended pregnancy. With a lack of research on the subject in Bangladesh, we aimed to examine the effect of unintended pregnancy on CoC. Methods Data from 4,493 mother-newborn dyads who participated in the cross-sectional 2014 Bangladesh Demographic and Health Survey were analysed. Women’s level of CoC was generated from responses to questions on the use and non-use of three recommended services during the course of pregnancy: four or more antenatal care (ANC) visits, skilled birth attendance (SBA) during delivery, and at least one postnatal care (PNC) visit within 24 hours of giving birth. Global recommendations of service use were used to classify CoC as high (used each of the recommended services), moderate (used at least two of the three recommended services), and low/none (no PNC, no SBA, and ≤3 ANC visits). Women’s pregnancy intention at the time of conception of their last pregnancy (ending with a live birth) was the major exposure variable, classified as wanted, mistimed, and unwanted. Unadjusted and adjusted (with individual-, household-, and community-level factors) multilevel multinomial logistic regression models were used to assess the association between unintended pregnancy and level of CoC. Results In Bangladesh, the highest level of CoC occurred in only 12% of pregnancies that ended with live births. This figure was reduced to 5.6% if the pregnancy was unwanted at conception. The antenatal period saw the greatest drop in CoC, with 65.13% of women receiving at least one ANC visit and 26.32% having four or more ANC visits. Following the adjustment of confounders, an unwanted pregnancy was found to be associated with 39% and 62% reduced odds of women receiving moderate and high levels of CoC, respectively, than those with a wanted pregnancy. Having a mistimed pregnancy was found to be associated with a 31% reduction in odds of women achieving a high CoC than women with a wanted pregnancy. Conclusion Almost nine in ten women did not achieve CoC in their last pregnancy, which was even higher when the pregnancy was unintended. Given that the ANC period has been identified as a critical time for intervention for these women, it is necessary for policies to scale up current maternal healthcare services that provide in-home maternal healthcare services and to monitor the continuity of ANC, with a particular focus on women who have an unintended pregnancy. Integration of maternal healthcare services with family planning services is also required to ensure CoC.
Role of a complex of two proteins in alleviating sodium ion stress in an economic crop

An economically valuable woody plant species tree bean (Cajanus cajan (L.) Millsp. ) is predominantly cultivated in tropical and subtropical areas and is regarded as an important food legume (or pulse) crop that is facing serious sodium ion stress. NAM (N-acetyl-5-methoxytryptamine) has been implicated in abiotic and biotic stress tolerance in plants. However, the role of NAM in sodium ion stress tolerance has not been determined. In this study, the effect of NAM was investigated in the economically valuable woody plant species, challenged with stress at 40 mM sodium ion for 3 days. NAM-treated plants (200 μM) had significantly higher fresh weight, average root length, significantly reduced cell size, increased cell number, and increased cytoskeleton filaments in single cells. The expression pattern of one of 10 Tree bean Dynamic Balance Movement Related Protein (TbDMP), TbDMP was consistent with the sodium ion-stress alleviation by NAM. Using TbDMP as bait, Dynamic Balance Movement Related Kinase Protein (TbDBK) was determined to interact with TbDMP by screening the tree bean root cDNA library in yeast. Biochemical experiments showed that NAM enhanced the interaction between the two proteins which promoted resist sodium ion stress resistance. This study provides evidence of a pathway through which the skeleton participates in NAM signaling.
Research on a New Type of Rigid-Flexible Coupling 3-DOF Micro-Positioning Platform

A new type of rigid-flexible coupling three degrees of freedom (3-DOF) micro-positioning platform with high positioning accuracy and high bearing capacity is developed, which consists of flexible drive mechanism and rigid platform. The flexible drive mechanism consists of three sets of symmetrical parallel round flexible hinge structures, each with a wedge structure in the middle of the symmetrical parallel flexible hinge. The rigid platform has an inclined plane with the same angle as the wedge, while the wedge structure is used to achieve the self-locking effect. The flexibility matrix method and ANSYS are used to analyze the statics of the flexible drive mechanism. The first four natural frequencies of the platform are obtained by dynamic simulation analysis. A symmetrical rigid flexible coupling micro-positioning platform experimental system is developed. Output characteristics, positioning accuracy, relationship between frequency and amplitude, and bearing performance of the micro-positioning platform are tested. These experimental results obviously show that the micro-positioning platform has good motion characteristics, high positioning accuracy, large movement distance, and large load bearing capacity performance.
The role of phytochemicals in sepsis: A mechanistic and therapeutic perspective

Sepsis and septic shock are still a leading cause of mortality and morbidity in intensive care units worldwide. Sepsis is an uncontrolled and excessive response of the innate immune system toward the invading infectious microbes, characterized by the hyper‐production of pro‐inflammatory mediators such as interleukin (IL)‐1β, IL‐6, tumor‐necrosis factor (TNF)‐α, and high‐mobility group box 1 (HMGB1). In severe sepsis, the overwhelming production of pro‐inflammatory cytokines and reactive oxygen species may compromise organ function and lead to the induction of abnormal apoptosis in different organs, resulting in multiple organ dysfunction syndrome and death. Hence, compounds that are able to attenuate inflammatory responses may have therapeutic potential for sepsis treatment. Understanding the pathophysiology and underlying molecular mechanisms of sepsis may provide useful insights in the discovery and development of new effective therapeutics. Therefore, numerous studies have invested much effort into elucidating the mechanisms involved with the onset and development of sepsis. The present review mainly focuses on the molecules and signaling pathways involved in the pathogenicity of sepsis. Additionally, several well‐known natural bioactive herbal compounds and phytochemicals, which have shown protective and therapeutic effects with regard to sepsis, as well as their mechanisms of action, are presented. This review suggests that these phytochemicals are able to attenuate the overwhelming inflammatory responses developed during sepsis by modulating different signaling pathways. Moreover, the anti‐inflammatory and cytoprotective activities of phytochemicals make them potent compounds to be included as complementary therapeutic agents in the diets of patients suffering from sepsis in an effort to alleviate sepsis and its life‐threatening complications, such as multi‐organ failure.
Factors facilitating or hindering meaningful staff–client interactions in people with intellectual disabilities and challenging behaviour: A systematic mixed studies review using thematic synthesis

Abstract Background Interactions with professional caregivers affect the quality of support and life of people with intellectual disabilities and contribute to the occurrence of challenging behaviour. The present literature review provides an overview of factors facilitating or hindering meaningful staff–client interactions in people with borderline to profound intellectual disabilities and challenging behaviour. Method Database searches, reference list and citation screening, and expert consultations were undertaken. A thematic synthesis of 28 studies was performed. Results Factors were identified at the client (i.e. behaviour, emotions and (dis)abilities), staff (i.e. interactive principles, knowledge, psychological resources, attributions, attitudes and (coping with) emotions) and context levels (i.e. group size, team and organization). Conclusions The present overview provides insights into factors that facilitate or hinder meaningful staff–client interactions with people with intellectual disabilities and challenging behaviour. The results support the need to combine client, staff and contextual factors when considering staff–client interactions in research and practice.
The multifaceted roles of nucleophagy in cancer development and therapy

Autophagy is an evolutionarily conserved process in which the cell degrades its own components and recycles the biomolecules for survival and homeostasis. It is an important cellular process to eliminate pathogens or damaged organelles. Nucleophagy, also termed as nuclear autophagy, is a more recently described subtype of autophagy, in which nuclear components, such as nuclear lamina and DNA, are to be degraded. Nucleophagy plays a double‐facet role in the development of cancer. On one hand, the clearance of damaged DNA or nuclear structures via autophagic pathway is crucial to maintain nuclear integrity and prevent tumorigenesis. On the other hand, in later stages of tumor growth, nucleophagy may facilitate cancer cell survival and metastasis in the nutrient‐depleted microenvironment. In this review, we discuss the relationship between nucleophagy and cancer along with potential intervention methods to target cancer through manipulating nucleophagy. Given the known observations about nucleophagy, it could be promising to target different nuclear components during the processes of nucleophagy, especially nuclear lamina. Further research on investigating the role of nucleophagy in oncological context could focus on dissecting its remaining molecular pathways and their connection to known tumor suppressors.
Systemic sclerosis and risk of cardiovascular disease

Supplemental Digital Content is available in the text Abstract Background: Systemic sclerosis (SSc) is an autoimmune disorder leading to extensive fibrosis and microvascular injury. Macrovascular disease is well documented in other autoimmune rheumatic diseases such as systemic lupus erythematosus and rheumatoid arthritis. However, the link is unclear between SSc and macrovascular disease, particularly atherosclerotic cardiovascular disease (CVD). This meta-analysis aimed to investigate the association between SSc and CVD. Methods: A thorough literature search was conducted in the Cochrane, Embase, Medline, and PubMed to identify all cohort studies comparing the risk of CVD with and without SSc. The pooled hazard ratios (HRs) with 95% confidence intervals (CIs) of cardiovascular end points were calculated. The risk of bias of included studies was assessed by the Newcastle-Ottawa scale. Results: Seven cohort studies with a total of 14,813 study participants were included. In a comparison of SSc patients versus non-SSc controls, the pooled HR for cardiovascular disease was 2.36 (95% CI 1.97–2.81); for peripheral vascular disease was 5.27 (95%CI 4.27–6.51); for myocardial infarction was 2.36 (95% CI 1.71–3.25); and for stroke was 1.52 (95% CI 1.18–1.96). Conclusion: This meta-analysis revealed that SSc was associated with an increased risk of CVD. Clinicians who manage patients with SSc should be aware of the increased cardiovascular burden and undertake preventive measures.
From in vitro towards in situ: structure‐based investigation of ABC exporters by electron paramagnetic resonance spectroscopy

ATP‐binding cassette (ABC) exporters have been studied now for more than four decades, and recent structural investigation has produced a large number of protein database entries. Yet, important questions about how ABC exporters function at the molecular level remain debated, such as which are the molecular recognition hotspots and the allosteric couplings dynamically regulating the communication between the catalytic cycle and the export of substrates. This conundrum mainly arises from technical limitations confining all research to in vitro analysis of ABC transporters in detergent solutions or embedded in membrane‐mimicking environments. Therefore, a largely unanswered question is how ABC exporters operate in situ, namely in the native membrane context of a metabolically active cell. This review focuses on novel mechanistic insights into type I ABC exporters gained through a unique combination of structure determination, biochemical characterization, generation of conformation‐specific nanobodies/sybodies and double electron–electron resonance.