Miracle-dz/UniFAR-FTUs huggingface dataset:
Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model

The gut microbiome plays an important role in the immune system development, maintenance of normal health status, and in disease progression. In this study, we comparatively examined the fecal microbiomes of Amish (rural) and non-Amish (urban) infants and investigated how they could affect the mucosal immune maturation in germ-free piglets that were inoculated with the two types of infant fecal microbiota (IFM). Differences in microbiome diversity and structure were noted between the two types of fecal microbiotas. The fecal microbiota of the non-Amish (urban) infants had a greater relative abundance of Actinobacteria and Bacteroidetes phyla, while that of the Amish (rural) counterparts was dominated by Firmicutes. Amish infants had greater species richness compared with the non-Amish infants' microbiota. The fecal microbiotas of the Amish and the non-Amish infants were successfully transplanted into germ-free piglets, and the diversity and structure of the microbiota in the transplanted piglets remained similar at phylum level but not at the genus level. Principal coordinates analysis (PCoA) based on Weighted-UniFrac distance revealed distinct microbiota structure in the intestines of the transplanted piglets. Shotgun metagenomic analysis also revealed clear differences in functional diversity of fecal microbiome between Amish and non-Amish donors as well as microbiota transplanted piglets. Specific functional features were enriched in either of the microbiota transplanted piglet groups directly corresponding to the predominance of certain bacterial populations in their gut environment. Some of the colonized bacterial genera were correlated with the frequency of important lymphoid and myeloid immune cells in the ileal submucosa and mesenteric lymph nodes (MLN), both important for mucosal immune maturation. Overall, this study demonstrated that transplantation of diverse IFM into germ-free piglets largely recapitulates the differences in gut microbiota structure between rural (Amish) and urban (non-Amish) infants. Thus, fecal microbiota transplantation to germ-free piglets could be a useful large animal model system for elucidating the impact of gut microbiota on the mucosal immune system development. Future studies can focus on determining the additional advantages of the pig model over the rodent model.
MArk: Exploiting Cloud Services for Cost-Effective, SLO-Aware Machine Learning Inference Serving

The advances of Machine Learning (ML) have sparked a growing demand of ML-as-a-Service: developers train ML models and publish them in the cloud as online services to provide low-latency inference at scale. The key challenge of ML model serving is to meet the response-time Service-Level Objectives (SLOs) of inference workloads while minimizing the serving cost. In this paper, we tackle the dual challenge of SLO compliance and cost effectiveness with MArk (Model Ark), a general-purpose inference serving system built in Amazon Web Services (AWS). MArk employs three design choices tailor-made for inference workload. First, MArk dy-namically batches requests and opportunistically serves them using expensive hardware accelerators (e.g., GPU) for improved performance-cost ratio. Second, instead of relying on feedback control scaling or over-provisioning to serve dynamic workload, which can be too slow or too expensive for inference serving, MArk employs predictive autoscaling to hide the provisioning latency at low cost. Third, given the stateless nature of inference serving, MArk exploits the ﬂexible, yet costly serverless instances to cover the occasional load spikes that are hard to predict. We evaluated the performance of MArk using several state-of-the-art ML models trained in popular frameworks including TensorFlow, MXNet, and Keras. Compared with the premier industrial ML serving platform SageMaker, MArk reduces the serving cost up to 7 . 8 × while achieving even better latency performance.
On the Specification of Term Values in Automatic Indexing

The existing practice in automatic indexing is reviewed, and it is shown that the standard theories for the specification of term values (or weights) are not adequate. New techniques are introduced for the assignment of weights to index terms, based on the characteristics of individual document collections. The effectiveness of some of the proposed methods is evaluated.
Action Research: A Guide for the Teacher Researcher

Chapter 1: Understanding Action Research Chapter 2: Deciding on an Area of Focus Chapter 3: Data Collection Techniques Chapter 4: Data Collection Considerations: Validity, Reliability, and Generalizability Chapter 5: Ethics Chapter 6: Data Analysis and Interpretation Chapter 7: Action Planning for Educational Change Chapter 8: Writing Up Action Research Chapter 9: Sharing, Critiquing, and Celebrating Action Research On-Line Appendix A: Action Research in Action: A Case Study of Curtis Elementary Appendix B: Descriptive Statistics and Action Research Appendix C: Displaying Data Visually
Predicting Protein Subcellular Localization using PsePSSM and Support Vector Machines

The prediction of protein subcellular localization (PSL) has been an important field of research. Many prediction systems nowadays have been developed that support the need. Most of these systems however focus on the development of new methods to describe a protein, which in turn can increase the prediction performance. In this paper,we propose a novel prediction system, an evolutionary algorithm based support vector machine for the prediction of PSL (ESVM-PSL) which aims to increase the prediction performance by optimizing SVMs. We apply ESVM-PSL to a set of proteins with jackknife validation. The prediction accuracy of SVMs is effectively increased from 48.9% to 67.5%. Our proposed method is also competitive with the previous systems in terms of prediction accuracy.
Early Risk Factors and Emotional Difficulties in Children at Risk of Developmental Language Disorder: A Population Cohort Study.

Purpose This study evaluated the pathways between developmental language disorder (DLD), psychosocial risk factors, and the development of emotional difficulties from ages 3 to 11 years within the Millennium Cohort Study. Method A total of 14,494 singletons (49.4% female) from the Millennium Cohort Study were evaluated within this study. Risk of DLD (rDLD) was defined as age 5 parent-reported language problems and/or -1.5 SDs on a Naming Vocabulary subtest at the age of 5 years. Children without rDLD formed the general population comparison group. Psychosocial risk factors included 9-month temperamental traits, parental psychological distress, and maternal attachment as well as age 3 emotional regulation abilities, parent-child relationship, and peer problems. The parent report Strengths and Difficulties Questionnaire Emotional Difficulty subscale at 3, 5, 7, and 11 years of age was the outcome variable. The trajectory of emotional difficulties was evaluated within a variable-centered approach and a person-centered approach, using growth mixture modeling. Results Children with rDLD ( n = 884) had increased levels of emotional problems when compared to the general population group ( n = 13,344). Psychosocial risk factors were increased in children with rDLD, fully mediated the increased emotional difficulties at 3 years, and partially mediated the increased emotional difficulties at 11 years. Children with rDLD were more likely to be included in emotional trajectory subgroups with an increasing pattern of emotional problems. rDLD was an additional risk factor for lower levels of emotional self-regulation and increased peer problems when controlling for the emotional difficulties trajectory subgroup. Conclusion This article indicates that the increased emotional difficulties found in children with rDLD are likely a function of early language difficulties influencing other domains of development, specifically social interactions (parent and peer) and emotional self-regulation abilities. Clinically, this reiterates the importance of early identification and treatment of children with language delays or clinical level language disorders. Supplemental Material https://doi.org/10.23641/asha.8323598.
Pattern recognition by cooperating neural networks

The study of connectionist models for pattern recognition is mainly motivated by their presumed simultaneous feature selection and classification. Character recognition is a common test case to illustrate the feature extraction and classification characteristics of neural networks. Most of the variability concerning size and rotation can be handled easily, while acquisition conditions are usually controlled. Many examples of neural character recognition applications were presented where the most successful results for optical character recognition (OCR) with image inputs were reported on a layered network (LeCun et al., 1990) integrating feature selection and invariance notions introduced earlier in neocognitron networks. Previously, we have presented a supervised learning algorithm, based on Kohonen's self- organizing feature maps, and its applications to image and speech processing (Midenet et al., 1991). From pattern recognition point of view, the first network performs local feature extraction while the second does a global statistical template matching. We describe these models and their comparative results when applied to a common French handwritten zip-code database. We discuss possible cooperation schemes and show that the performances obtained by these networks working in parallel exceed those of the networks working separately. We conclude by the possible extensions of this work for automatic document processing systems.
The role of the antidiabetic drug metformin in the treatment of endocrine tumors.

Incidence of endocrine cancers is rising every year. Over the last decade, evidence has accumulated that demonstrates the anti-cancer effects of an anti-diabetic drug - metformin - in endocrine malignancies. We performed a literature review utilizing the Pubmed, Medline and clinicaltrials.gov databases using the keyword "metformin" plus the following terms: "thyroid cancer," "thyroid nodules," "parathyroid," "hyperparathyroidism," "adrenal adenoma," "Cushing syndrome," "hyperaldosteronism," "adrenocortical cancer," "neuroendocrine tumor (NET)," "pancreatic NET (pNET)," "carcinoid," "pituitary adenoma," "pituitary neuroendocrine tumor (PitNET)", "prolactinoma," "pheochromocytoma/paraganglioma. " We found 37 studies describing the preclinical and clinical role of metformin in endocrine tumors. The available epidemiological data shows an association between exposure of metformin and lower incidence of thyroid cancer and pNETs in diabetic patients. Metformin treatment has been associated with better response to cancer therapy in thyroid cancer and pNETs. Preclinical evidence suggests that the primary direct mechanisms of metformin action include inhibition of mitochondrial oxidative phosphorylation via inhibition of both mitochondrial complex I and mitochondrial glycerophosphate dehydrogenase, leading to metabolic stress. Decreased ATP production leads to an activation of a cellular energy sensor, AMPK, and subsequent downregulation of mTOR signaling pathway, which is associated with decreased cellular proliferation. We also describe several AMPK-independent mechanisms of metformin action, as well as the indirect mechanisms targeting insulin resistance. Overall, repositioning of metformin has emerged as a promising strategy for adjuvant therapy of endocrine tumors. The mechanisms of synergy between metformin and other anti-cancer agents need to be elucidated further to guide well-designed prospective trials on combination therapies in endocrine malignancies.
CARD9 downregulation suppresses the growth of oral squamous cell carcinoma by regulating NF-κB.

OBJECTIVE To discover the expression pattern and potential underlying mechanism of the caspase recruitment domain containing protein 9 (CARD9) in oral squamous cell carcinoma (OSCC). METHODS CARD9 expression was detected by qRT-PCR and Western blot in OSCC tissues and cells, and OSCC (CGHNC9 and OECM-1) cell lines were divided into Control, NC siRNA and CARD9 siRNA groups. Then, MTT, flow cytometry, wound-healing and Transwell assays were carried out to determine the changes in cellular biological characteristics. Immunoblot assay was performed for the expressions of NF-κB pathway. Finally, we constructed the xenograft models in nude mice to validate the in-vivo effect of CARD9 siRNA on OSCC cell growth. RESULTS CARD9 was up-regulated in both OSCC tissues and cells, exhibiting a close relation with major clinicopathological features of OSCC patients. Transfection of CARD9 siRNA inhibited the proliferation, migration and invasion of OSCC cells with the enhanced cell apoptosis, and meanwhile, CARD9, p-p65/p65, p-IKKα/IKKα and p-IkBα/IkBα were downregulated. The tumor formation assay on nude mice also suggested that CARD9 siRNA might block the in-vivo growth of OSCC cells. CONCLUSION CARD9 suppression results in the up-regulation of NF-κB pathway with suppressed proliferation, migration and invasion of OSCC cells, and facilitates the apoptosis. This article is protected by copyright. All rights reserved.
Comparing point shear wave elastography (ElastPQ) and transient elastography for diagnosis of fibrosis stage in non‐alcoholic fatty liver disease

Transient elastography (TE) and point shear wave elastography (pSWE) are noninvasive methods to diagnose fibrosis stage in patients with chronic liver disease. The aim of this study is to compare the accuracy of the two methods to diagnose fibrosis stage in non‐alcoholic fatty liver disease (NAFLD) and to study the intra‐observer and inter‐observer variability when the examinations were performed by healthcare personnel of different backgrounds.
Measuring individual differences in task‐related motivation in children and adolescents: Development and validation of a new self‐report measure

Task characteristics can alter motivation. Understanding how individuals respond to these characteristics is important in understanding how to adapt tasks to increase engagement of individuals with mental health problems. We describe the development of a self‐report questionnaire quantifying individual differences in task‐related motivation—The Child and Adolescent Motivational Profile (CHAMP). We explore the association with externalizing/internalizing problems.
Hallucinations, somatic‐functional disorders of PD‐DLB as expressions of thalamic dysfunction

Hallucinations, delusions, and functional neurological manifestations (conversion and somatic symptom disorders) of Parkinson's disease (PD) and dementia with Lewy bodies increase in frequency with disease progression, predict the onset of cognitive decline, and eventually blend with and are concealed by dementia. These symptoms share the absence of reality constraints and can be considered comparable elements of the PD‐dementia with Lewy bodies psychosis. We propose that PD‐dementia with Lewy bodies psychotic disorders depend on thalamic dysfunction promoting a theta burst mode and subsequent thalamocortical dysrhythmia with focal cortical coherence to theta electroencephalogram rhythms. This theta electroencephalogram activity, also called fast‐theta or pre‐alpha, has been shown to predict cognitive decline and fluctuations in Parkinson's disease with dementia and dementia with Lewy bodies. These electroencephalogram alterations are now considered a predictive marker for progression to dementia. The resulting thalamocortical dysrhythmia inhibits the frontal attentional network and favors the decoupling of the default mode network. As the default mode network is involved in integration of self‐referential information into conscious perception, unconstrained default mode network activity, as revealed by recent imaging studies, leads to random formation of connections that link strong autobiographical correlates to trivial stimuli, thereby producing hallucinations, delusions, and functional neurological disorders. The thalamocortical dysrhythmia default mode network decoupling hypothesis provides the rationale for the design and testing of novel therapeutic pharmacological and nonpharmacological interventions in the context of PD, PD with dementia, and dementia with Lewy bodies. © 2019 International Parkinson and Movement Disorder Society
Mechanics of nuclear membranes

ABSTRACT Cellular nuclei are bound by two uniformly separated lipid membranes that are fused with each other at numerous donut-shaped pores. These membranes are structurally supported by an array of distinct proteins with distinct mechanical functions. As a result, the nuclear envelope possesses unique mechanical properties, which enables it to resist cytoskeletal forces. Here, we review studies that are beginning to provide quantitative insights into nuclear membrane mechanics. We discuss how the mechanical properties of the fused nuclear membranes mediate their response to mechanical forces exerted on the nucleus and how structural reinforcement by different nuclear proteins protects the nuclear membranes against rupture. We also highlight some open questions in nuclear envelope mechanics, and discuss their relevance in the context of health and disease. Summary: This paper reviews literature related to nuclear membrane mechanics and its importance in envelope function.
The Long-term Efficacy of Sodium Glucose Co-transporter 2 Inhibitor in Patients with Non-alcoholic Fatty Liver Disease

Objective Sodium glucose co-transporter 2 inhibitor (SGLT-2i), recommended for patients with type 2 diabetes, has been reported to improve the liver function test results in non-alcoholic fatty liver disease (NAFLD). However, the long-term effects of SGLT-2i on the liver function and body weight in NAFLD patients have not been fully elucidated. In this study, we investigated the long-term effects of SGLT-2i in NAFLD patients. Methods Twenty-two diabetic patients with NAFLD were enrolled in this study. We assessed the body weight, liver enzyme levels, metabolism, and glucose levels at 12 months (22 cases) and 24 months (15 cases) after the initiation of SGLT-2i. The changes in controlled attenuation parameter (CAP) and liver stiffness in 20 of the 22 patients were evaluated using transient elastography (TE) and acoustic radiation force impulse (ARFI) elastography before the initiation of treatment and 1 year later. Results Body weight and aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels were significantly decreased at 12 and 24 months after SGLT-2i treatment. The decrease in the levels of ALT at 12 and 24 months was significantly correlated with the level of ALT at the initiation of SGLT-2i (r=0.813, p=0.001 and r=0.867, p=0.0001, respectively). SGLT-2i also reduced the CAP and velocity of shear wave (Vs) values at 12 months (CAP 315.1±43.4 db/mL→293.1±27.2 db/mL, p=0.027; Vs 1.87±0.8 m/s→ 1.48±0.6 m/s, p=0.011). Conclusion SGLT-2i treatment improved the liver function test results and reduced the body weight in NAFLD patients over a period of 12-24 months. This improvement was greater in patients with higher ALT values at baseline than in those with lower values.
Urologic Injury and Fistula After Hysterectomy for Benign Indications.

OBJECTIVE To explore the rates and risk factors for sustaining a genitourinary injury during hysterectomy for benign indications. METHODS In this population-based cohort study, all women who underwent hysterectomy for benign indications were identified from the Office of Statewide Health Planning and Development databases in California (2005-2011). Genitourinary injuries were further classified as identified at the time of hysterectomy, identified after the date of hysterectomy; or unidentified until a fistula developed. RESULTS Of the 296,130 women undergoing hysterectomy for benign indications, there were 2,817 (1.0%) ureteral injuries, 2,058 (0.7%) bladder injuries and 834 (0.3%) genitourinary fistulas (80/834 of which developed after an injury repair). Diagnosis was delayed in 18.6% and 5.5% of ureteral and bladder injuries, respectively. Subsequent genitourinary fistula development was lower if the injury was identified immediately (compared with delayed) for both ureteral (0.7% vs 3.4% odds ratio [OR] 0.28; 95% CI 0.14-0.57) and bladder injuries (2.5% vs 6.5% OR 0.37; 95% CI 0.16-0.83). Indwelling ureteral stent placement alone was more successful in decreasing the risk of a second ureteral repair for immediately recognized ureteral injuries (99.0% vs 39.8% for delayed injuries). With multivariate adjustment, prolapse repair (OR 1.44, 95% CI 1.30-1.58), an incontinence procedure (OR 1.40, 95% CI 1.21-1.61), mesh augmented prolapse repair (OR 1.55, 95% CI 1.31-1.83), diagnosis of endometriosis (OR 1.46, 95% CI 1.36-1.56), and surgery at a facility in the bottom quartile of hysterectomy volume (OR 1.37, 95% CI 1.01-1.89) were all associated with an increased likelihood of a genitourinary injury. An exclusively vaginal (OR 0.56, 95% CI 0.53-0.64) or laparoscopic (OR 0.80, 95% CI 0.75-0.86) approach was associated with lower risk of a genitourinary injury as compared with an abdominal approach. CONCLUSION Genitourinary injury occurs in 1.8% of hysterectomies for benign indications; immediate identification and repair is associated with a reduced risk of subsequent genitourinary fistula formation.
Large-Scale Benchmark of Exchange–Correlation Functionals for the Determination of Electronic Band Gaps of Solids

We compile a large data set designed for the efficient benchmarking of exchange–correlation functionals for the calculation of electronic band gaps. The data set comprises information on the experimental structure and band gap of 472 nonmagnetic materials and includes a diverse group of covalent-, ionic-, and van der Waals-bonded solids. We used it to benchmark 12 functionals, ranging from standard local and semilocal functionals, passing through meta-generalized-gradient approximations, and several hybrids. We included both general purpose functionals, like the Perdew–Burke–Ernzerhof approximation, and functionals specifically crafted for the determination of band gaps. The comparison of experimental and theoretical band gaps shows that the modified Becke–Johnson is at the moment the best available density functional, closely followed by the Heyd–Scuseria–Ernzerhof screened hybrid from 2006 and the high-local-exchange generalized-gradient approximation.
2. RESEARCH IN THE TEACHING OF SPEAKING

This chapter reviews research and practice in six main areas relevant to the teaching of speaking: (1) the growing influence of spoken corpora, (2) the debates concerning native speaker (NS) and nonnative speaker (NNS) models for spoken pedagogy,(3) the issue of authenticity in spoken materials, (4) approaches to understanding speaking in the classroom, (5) the selection of texts and aspects of spoken language for the teaching of speaking, and (6) developments in materials and methods for the teaching of speaking. Spoken corpora, whether NS corpora collected in “old” or “new” variety locations or NNS corpora based on learner data or expert/successful user data, have generated vigorous debate as to how spoken language should be modeled for teaching, and their influence is being seen in shifts in methodology toward language-awareness-based approaches as well as new materials based on lexicogrammatical and discoursal corpus evidence. Various approaches to understanding classroom speaking are also reviewed, including discourse analysis, conversation analysis, cognitive approaches, and the Vygotskian perspective. Applications of insights from these approaches are reviewed, especially how the approaches affect the selection of texts and language features to be taught. Finally, practical discussion on the teaching of specific spoken genres is reviewed and probable future directions are discussed.