Miracle-dz/UniFAR-FTUs huggingface dataset:
Context dependency and saturating effects of loss of rare soil microbes on plant productivity

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.
Profiles of self-evaluation as a metacognitive skill: An indicator of rehabilitation potential among people with schizophrenia.

OBJECTIVE The purpose of this study is to identify subgroups of people with schizophrenia on the basis of self-assessment accuracy (metacognition) and examine group differences in rehabilitation potential. METHOD Participants were 51 individuals with schizophrenia-spectrum disorders recruited from community mental health centers. Data from a self-report measure of cognition and a neuropsychological battery were compared and utilized to place participants in 3 accuracy groups: overestimators, accurate estimators, and underestimators. A multivariate analysis of variance was used to compare performance between accuracy groups on an index of rehabilitation potential. RESULTS Three distinct profiles of metacognitive ability were identified. The analysis found that participants who underestimated their cognitive functioning had the highest scores on an index of rehabilitation potential (learning potential), and those who overestimated their functioning had the lowest. No significant differences in diagnostic or sociodemographic variables were found among accuracy groups. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE Results suggest that there are differences in the way people with schizophrenia evaluate their cognition and, further, these metacognitive profiles are associated with differences in the ability to learn new tasks quickly. Thus, identifying subgroups of individuals based on metacognitive processing may help identify those most likely to benefit from cognitive remediation and other rehabilitative therapies. Future research should explore the link between metacognitive ability and rehabilitation potential in greater detail. Future investigations should also clarify the implications that underestimation of ability has for overall recovery and quality of life in people with schizophrenia. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Testing can facilitate forgetting of tested items

Abstract Previous research has shown that taking a test facilitates memory retention on later retesting, although facilitation is stronger when retesting is delayed. On the basis of the finding that testing prevents later forgetting without affecting memory recovery, we investigated immediate effects of taking a test on retrievability of a tested item. In two experiments, forty participants recalled studied items, then performed a retest of the studied items (test condition) and a non-episodic-memory task (distractor condition), and immediately afterward re-recalled the items. The test condition elicited more item losses (i.e. forgetting) than the distractor condition, whereas there were no condition differences in the number of item gains (i.e. remembering) and recall clustering. These results suggest that taking a test on a target item facilitates forgetting of the very same item for a short interval of time, a possible reason for the late appearance of the testing effect.
Using BERT and Semantic Patterns to Analyze Disease Outbreak Context over Social Network Data

: Predicting disease outbreaks has been a focus for various institutions and researchers for many years. However, any models that seemed to get close to resolve this issue have failed to predict potential outbreaks with accuracy over time. For leveraging the social media data effectively, it is crucial to ﬁlter out noisy information from the large volume of data ﬂux so that we could better estimate potential disease outbreaks with growing social data. Not satisﬁed with essential keyword-based ﬁltration, many researchers turn to machine learning for a solution. In this paper, we apply deep learning techniques to address the Tweets classiﬁcation problem concerning disease outbreak predictions. To achieve this, we curated a labeled corpus of Tweets that reﬂect different types of disease-related reports, showcasing diverse community sentiment and varied potential us-ages in emergency responses. Further, we used BERT, a word embedding and deep learning method to apply transfer learning against our curated dataset. Applying BERT showed that it performs better in comparable results to Long short-term memory (LSTM) and outperforming the baseline model on average in terms of accuracy and F-score.
The effect of light-activated antimicrobial agents on bacterial virulence factors and key modulators of inflammation

Photodynamic therapy is a promising new strategy for the treatment of superficial skin infections and periodontitis. A limitation of antibiotic treatment for these diseases is that even after successful killing of the infecting organism, secreted virulence factors may still be present and cause significant damage to host tissues. If light-activated antimicrobial agents can inactivate microbial virulence factors in addition to killing the pathogenic microorganisms, this would represent an advantage of photodynamic therapy over conventional treatment options. The light-activated antimicrobial agents methylene blue and tin chlorin e6 in combination with laser light of 665 and 633 nm respectively, were assessed for their antibacterial activity and ability to reduce the activity of selected virulence factors of Staphylococcus aureus and Porphyromonas gingivalis. In addition to successfully reducing the microbial burden, it was demonstrated that photosensitisation was able to cause significant reductions in the activity of a number of secreted and cell wall-associated virulence factors produced by these species when irradiated with laser light of the appropriate wavelength. Photosensitisation was also shown to reduce the biological activities of the proinflammatory cytokines tumour necrosis factor-alpha and interleukin-6, which are produced in response to infecting bacteria and are associated with damage to host tissues. The results of these studies indicate that light-activated antimicrobial agents may be useful in reducing the pathology associated with bacterial virulence factors and host-mediated inflammation when used as part of an antimicrobial treatment regimen.
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In this paper, we present a practical framework for the syntactic transfer of compoundcomplex sentences from English to Hindi in the context of a transfer-based Machine Assisted Translation (MAT) system. The analysis is based on the linguistic intuitions of the authors, backed by evidence from a real-life corpus, and ongoing work on a building a practical MAT system. The description of the framework is based on a template-like representation. However, the ideas expressed are essentially independent of the formalism or the representation. The most important component of the framework is the mapping of finite as well as nonfinite verb groups, in order to cover both simple as well as compound-complex sentences. Due to the differences in style and structure between English and Hindi, this mapping is non-trivial. We describe the major issues involved and suggest strategies for handling them.
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This paper is the written counterpart to a presentation given in Ha Noi, Vietnam, May 15, 2008 during the United Nations Day of Vesak 2008 Convention, on the effects of war and healing. The paper introduces the work of the Harvard Program in Refugee Trauma (HPRT) located in Boston, Massachusetts. It describes the HPRT Global Mission of education and capacity building of health care professionals, international relief workers and policy makers in the area of mental health in nations suffering post-conflict and disaster recovery. In particular the paper discusses the HPRT’s unique approach to assisting individuals with severe traumatic histories as seen through the lens of the author’s work as a psychopharmacologist with Southeast Asians and a team member of the HPRT in Lynn, Massachusetts, through the Lynn Community Health Center (LCHC). LCHC is a multi-disciplinary outpatient health service clinic located north of Boston, Massachusetts. Many patients who have survived genocide, torture, imprisonment, and war suffer from chronic Post Traumatic Stress Disorder (PTSD) with the sequellae of depression, nightmares, inability to work gainfully, and panic anxiety. Two stories of actual patients (their identifying data protected) are presented to illustrate self-healing and the role of mindfulness, the function of memory in storytelling and recovery, and the value of spirituality, work and altruism in healing. 106 R OBERT B RIAN W ALL H UMAN A RCHITECTURE : J OURNAL OF THE S OCIOLOGY OF S ELF -K NOWLEDGE , VI, 3, S UMMER 2008 T HE H ARVARD P ROGRAM IN
The Effect of Physical Activity on Human Milk Macronutrient Content and Its Volume.

Objective: There are multiple health benefits associated with both breastfeeding and practicing physical activity (PA). Therefore, it is likely that many women might want to engage in both. We designed the current randomized clinical trial to examine the effect of moderate- to high-intensity PA on human milk (HM) volume and macronutrient contents. Methods and Study Design: In this prospective, randomized, crossover clinical trial, we recruited 31 healthy mothers who had been exclusively breastfeeding their infants. Mothers expressed HM twice each day on 2 consecutive days-a day with PA (1-hour before and 1-hour after PA) and a control day without PA (at the exact same hours of the day). The order of days (with/without PA) was determined randomly. Macronutrients and energy contents of HM were analyzed using the Human Milk Analyzer (Miris AB, Uppsala, Sweden). PA was graded according to the Borg Rating of Perceived Exertion scale (RPE scale). Results: A total 124 HM samples from 31 mothers were analyzed. Moderate- to high-intensity PA affected neither macronutrients (fat, carbohydrates, protein) nor energy content. Milk volume remained unaffected by PA as well. Conclusions: Maternal PA does not affect HM volume or its macronutrient contents. Lactating mothers can be reassured regarding their breast milk volume and composition while practicing PA of moderate to high intensity.
SCRaMbLEing of a synthetic yeast chromosome with clustered essential genes reveals synthetic lethal interactions.

Genome-scale gene knockout is an important approach to the study of global genetic interactions. SCRaMbLEing of synthetic yeast chromosomes provides an efficient way to generate random deletion mutants. Here, we demonstrate the use of SCRaMbLE to explore synthetic lethal interactions. First, all essential genes of yeast chromosome III (chrIII) were clustered in a centromeric plasmid. We found that three types of reorganized clustered chrIII essential genes had similar transcriptional levels. Further, SCRaMbLEing of synthetic chromosome III (synIII) with supplementary of the clustered essential genes enables deletion of large chromosomal regions. Investigation of 141 SCRaMbLEd strains revealed varied deletion frequencies of synIII chromosomal regions. Among the undeletable regions, a hidden synthetic lethal interaction was revealed in the region of synIII 82-88kb. This study shows that SCRaMbLE with clustered essential genes enhances streamlining of synthetic yeast chromosome and provides a novel strategy to uncover complex genetic interactions.
Age- and Sex-Associated Changes in mRNA Expression of Neurodegenerative Disorder-Related Molecules in the Hippocampus and Cerebellum of Rat Brain

ii ACKNOWLEDGEMENTS I would like to take this opportunity to thank each and everyone who helped me to achieve my Master's degree. First and foremost, I would like to dedicate my work to the God I believe Sri Venkateswara swamy and my parents, Venkaiah Thulluri and Koteswaramma Thulluri for what I am today. They have given me strength day after day. If it were not for them, I would not have made it this far. I would like to express my sincere gratitude to my advisor, Dr. Bin Wang, for instilling in me the qualities of being a good researcher. Her infectious enthusiasm and unlimited zeal have been major driving forces through my graduate career at Marshall University. My Master's committee members, Dr. Eric R Blough, Dr. Leslie Frost and Dr.Miaozong Wu, deserve special thanks for helping me to undo the knots in my research and critical evaluation of my research progress. Also thanks to Dr. Eric Blough for readily donating the Rat brain tissue samples. Thanks also go to all of my great teachers who have taught me in High School, College level and Marshall University. Thanks to all my lab members who have helped me. Thanks to all my extended family members here in Huntington. Life was fabulous with you people and was always fun, it was as if I am in my motherland. Siva, Nandu and Anu. Thanks are due to my friends in other places who have helped me reach this day. Finally I would like to thank the Marshall University Department of Chemistry for giving me this opportunity to conduct and present my Master's research Project.
Vitamin D Deficiency in a Portuguese Cohort of Patients with Inflammatory Bowel Disease: Prevalence and Relation to Disease Activity

Background and Aims: Vitamin D deficiency is more common in inflammatory bowel disease (IBD) patients than in the general population. However, there are conflicting data about predictive factors of vitamin D deficiency and its potential association with disease activity. The aims of this study were to determine the prevalence and predictive factors of vitamin D deficiency and to evaluate a possible association with disease activity. Methods: A prospective observational study was conducted, including patients with IBD from January to July 2016. The Endocrine Society guidelines were considered for defining levels of serum 25-hydroxyvitamin D (25-OH-D) as follows: deficient (< 20 ng/mL, < 10 ng/mL being severe deficiency), insufficient (21–29 ng/mL), and adequate (> 30 ng/mL). Results: A total of 152 patients (52% men; 47.2 ± 17.3 years) were included, of whom 70% had Crohn’s disease (CD). Thirty-seven percent of patients were on immunosuppressors and 17% were on biologics. The majority were outpatients (88.2%). Mean 25-OH-D levels were 17.1 ± 8 ng/mL (CD: 16.7 ± 8 ng/mL vs. ulcerative colitis: 17.6 ± 7 ng/mL, p = 0.1). Inadequate levels were present in 90.8% of patients (deficiency: 68.4%; insufficiency: 22.4%). A significant negative correlation between 25-OH-D levels and age (r = –0.2, p = 0.04), C-reactive protein (CRP) levels (r = –0.22, p = 0.004), and Harvey-Bradshaw index (HBi) (r = –0.32, p = 0.001) was found. Patients with severe deficiency showed a higher CRP (0.6 vs. 1.4 mg/dL, p = 0.03), erythrocyte sedimentation rate (ESR) (22 vs. 31 mm/h, p = 0.03), and HBi (2 vs. 5, p < 0.001) and lower hemoglobin (13.6 vs. 12.7 g/dL, p = 0.02). There was no association between vitamin D deficiency and gender, type, extent, and duration of disease, surgery, and other measures of disease activity, such as ESR, hemoglobin (these 2 items except for severe deficiency), fecal calprotectin, or Truelove and Witts classification. Conclusions: There is a high prevalence of inadequate levels of vitamin D in IBD patients, particularly deficiency (68.4%). There seems to exist an association between lower levels of vitamin D and higher disease activity, especially in CD.
Engineering prokaryotic transcriptional activator XylR as a xylose-inducible biosensor for transcription activation in yeast.

Biosensors regulated by specific substrates are needed to develop genetic tools to meet the needs of engineering microbial cell factories. Here, a xylose-inducible biosensor (Xylbiosensor), comprising the Escherichia coli activation factor XylR, fusion activation domain (AD) VPRH, and a hybrid promoter with operator xylO, was established in Yarrowia lipolytica. Addition of xylose to an engineered Y. lipolytica strain harboring the Xylbiosensor could trigger significant transcriptional activation of target genes, such as mcherry and the xylose utilization gene. Furthermore, a novel promoter Pleu-Pxo-Ptef was developed to construct a bi-directional expression system. The Xylbiosensor showed good portability in Saccharomyces cerevisiae, suggesting its potential value in other eukaryotic cells. This study is the first to construct a "turn-on" Xylbiosensor induced by xylose addition based on a prokaryotic activator XylR and eukaryotic universal AD. The Xylbiosensor exhibits potential in pathway engineering for xylose utilization and xylose-derived product biosynthesis in yeast.
ROLE OF ING2 (INHIBITOR OF GROWTH FAMILY MEMBER 2) IN CELLUAR RESPONSES TO DNA DAMAGE

Genome stability is essential for cells to survive. Consequently, cells have evolved intricate responses that include transcriptional changes, cell-cycle arrest, activation of DNA repair, and apoptosis. Such responses prevent permanent fixation of DNA damage induced by genotoxic agents into the genome, thus contributing to genome stability. A collection of proteins implicated in DNA damage responses are called Inhibition of Growth (ING) family, which are a group of small molecular weight proteins that regulate a variety of biological functions ranging from senescence, cell cycle arrest, apoptosis and DNA repair. ING proteins interact with Histone Acetyl-transferases (HAT) and Histone Deacetylases (HDAC) to alter the state of chromatin compaction and acetylation status of many proteins during DNA damage. A specific member of the ING family, ING2 has been implicated in modulating the tumor suppressor, p53 function through p300 HAT-mediated acetylation. Irradiation fails to upregulate ING2, but increases its association with transcription co-activator p300. That p300 HAT activation in the cells with ING2 knock down is hampered post-irradiation suggests that the interaction between ING2 and p300 is indispensable for the upregulation of the p300 HAT activity. Cells deficient in protein kinase Ataxia Telangiectasia Mutated (ATM) displays impaired p300 HAT activation and less association between p300 and ING2 following ionizing radiation, indicating that ATM function is also required. Alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) upregulates ING2 level in both time- and dose-dependent manner. We further observed that ING2 regulates the cell death response induced by this alkylator through a mechanism involving acetylation and stabilization of p73. Induction/acetylation of p53, in response to MNNG, however, proceeds in an ING2-independent manner. Inhibition of c-Abl by STI571 treatment blocked ING2 upregulation and p73 acetylation induced by MNNG. Similarly, MLH1- suppressed or mutated cells displayed defective ING2 upregulation and p73 acetylation in response to MNNG, which suggests that Mlh1- and c-Abl-dependent upregulation of ING2 activates the cell death response to MNNG through p73 acetylation.Taken together, these findings demonstrate that ING2 plays an important role in the cellular responses to different DNA damage by regulating the acetylation of tumor suppressors.
Rotterdam criteria, the end

Rotterdam criteria According to the Rotterdam consensus, 1 polycystic ovarian syndrome (PCOS) is defined by the presence of two of three of the following criteria: oligo-anovulation, hyperandrogenism and polycystic ovaries (≥ 12 follicles measuring 2-9 mm in diameter and/or an ovarian volume > 10 mL in at least one ovary). The sonographic criteria were based on a study published in 2003 by Jonard et al., where patients with PCOS were found to have significantly more follicles in the 25 mm range than a control group comprised of women with tubal or male factor infertility. The decision to set the cut-off at 12 follicles measuring between 2 and 9 mm resulted from a compromise between specificity (99%) and sensitivity (75%), noting that narrowing the range to between 2 and 5 mm did not improve the diagnostic power. A suggestion was made to repeat the assessment in a subsequent cycle if the ovary was enlarged and its antral follicle count obscured by a dominant follicle (>10 mm) or a corpus luteum. There is no consensus on how to classify ovaries with a high follicle count when using oral contraception or other exogenous hormones or when there is evidence of a dominant follicle or corpus luteum in successive cycles.
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# In this work, a dynamic model of emulsion polymerization processes is extended by the inclusion of vaporization from the liquid phases in the reactor to the gaseous phase. The multi-component gas-liquid mass transfer phenomenon is described by a set of algebraic equations which are solved by an iterative procedure. The vaporization fluxes are described by Maxwell-Stefan's diffusion equations. Based upon the extended model, a novel operation strategy is developed. By controlled vaporization, additional heat is removed from the reaction system. This makes it possible to extend the restrictions imposed by the limited heat removal by the cooling jacket considerably. Simulation results are presented for the homopolymerization of vinyl acetate in an industrial scale reactor operated in semi-batch mode. The results show that a significant amount of heat can be removed by evaporative cooling.
Chloride accumulation in endosomes and lysosomes: facts checked in mice

Loss of the ClC‐3 chloride/proton exchanger found in intracellular compartments leads to marked neurodegeneration. New genetic work by Weinert et al (2020) now shows that selective impairment of ClC‐3's ion exchange activity is sufficient to elicit this severe phenotype in vivo. ClC‐3 cooperates with the closely related ClC‐4 in protecting endolysosomal chloride balance and neuronal integrity.