Miracle-dz/UniFAR-FTUs huggingface dataset:
Blautia coccoides JCM1395T Achieved Intratumoral Growth with Minimal Inflammation: Evidence for Live Bacterial Therapeutic Potential by an Optimized Sample Preparation and Colony PCR Method

We demonstrate that Blautia coccoides JCM1395T has the potential to be used for tumor-targeted live bacterial therapeutics. Prior to studying its in vivo biodistribution, a sample preparation method for reliable quantitative analysis of bacteria in biological tissues was required. Gram-positive bacteria have a thick outer layer of peptidoglycans, which hindered the extraction of 16S rRNA genes for colony PCR. We developed the following method to solve the issue; the method we developed is as follows. The homogenates of the isolated tissue were seeded on agar medium, and bacteria were isolated as colonies. Each colony was heat-treated, crushed with glass beads, and further treated with restriction enzymes to cleave DNAs for colony PCR. With this method, Blautia coccoides JCM1395T and Bacteroides vulgatus JCM5826T were individually detected from tumors in mice intravenously receiving their mixture. Since this method is very simple and reproducible, and does not involve any genetic modification, it can be applied to exploring a wide range of bacterial species. We especially demonstrate that Blautia coccoides JCM1395T efficiently proliferate in tumors when intravenously injected into tumor-bearing mice. Furthermore, these bacteria showed minimal innate immunological responses, i.e., elevated serum tumor necrosis factor α and interleukin-6, similar to Bifidobacterium sp. , which was previously studied as a therapeutic agent with a small immunostimulating effect.
Seismology of active regions: Current status and perspectives

The goal of helioseismology is to provide accurate information about the Sun’s interior from the observations of the wave field at its surface. In the last three decades, both global and local helioseismology studies have made significant advances and breakthroughs in solar physics. However, 3-d mapping of the structure and dynamics of sunspots and active regions below the surface has been a challenging task and is among the long standing and intriguing puzzles in solar physics due to the complexity of the turbulent and dynamic nature of magnetized regions. In this review, I present some of the recent results relevant for helioseismology of sunspots and active regions obtained from high resolution observations, forward modeling and numerical simulations.
Estimation of Knee Assistive Moment in a Gait Cycle Using Knee Angle and Knee Angular Velocity through Machine Learning and Artificial Stiffness Control Strategy (MLASCS)

Nowadays, many people around the world cannot walk perfectly because of their knee problems. A knee-assistive device is one option to support walking for those with low or not enough knee muscle forces. Many research studies have created knee devices with control systems implementing different techniques and sensors. This study proposes an alternative version of the knee device control system without using too many actuators and sensors. It applies the machine learning and artificial stiffness control strategy (MLASCS) that uses one actuator combined with an encoder for estimating the amount of assistive support in a walking gait from the recorded gait data. The study recorded several gait data and analyzed knee moments, and then trained a k-nearest neighbor model using the knee angle and the angular velocity to classify a state in a gait cycle. This control strategy also implements instantaneous artificial stiffness (IAS), a control system that requires only knee angle in each state to determine the amount of supporting moment. After validating the model via simulation, the accuracy of the machine learning model is around 99.9% with the speed of 165 observers/s, and the walking effort is reduced by up to 60% in a single gait cycle.
Replication of Real-World Evidence in Oncology Using Electronic Health Record Data Extracted by Machine Learning

Simple Summary Obtaining and structuring information about the characteristics, treatments, and outcomes of people living with cancer for research purposes is difficult and resource-intensive. Oftentimes, this information can only be found in electronic health records (EHRs). In response, researchers use natural language processing with machine learning (ML extraction) techniques to extract information at scale. This study evaluated the quality and fitness-for-use of EHR-derived oncology data curated using ML extraction, relative to the standard approach, abstraction by trained experts. Using patients with lung cancer from a real-world database, we performed replication analyses demonstrating common analyses conducted in observational research. Eligible patients were selected into biomarker- and treatment-defined cohorts, first with expert-abstracted then with ML-extracted data. The study’s results and conclusions were similar regardless of the data curation method used. These results demonstrate that high-performance ML-extracted variables trained on expert-abstracted data can achieve similar results as when using abstracted data, unlocking the ability to perform oncology research at scale. Abstract Meaningful real-world evidence (RWE) generation requires unstructured data found in electronic health records (EHRs) which are often missing from administrative claims; however, obtaining relevant data from unstructured EHR sources is resource-intensive. In response, researchers are using natural language processing (NLP) with machine learning (ML) techniques (i.e., ML extraction) to extract real-world data (RWD) at scale. This study assessed the quality and fitness-for-use of EHR-derived oncology data curated using NLP with ML as compared to the reference standard of expert abstraction. Using a sample of 186,313 patients with lung cancer from a nationwide EHR-derived de-identified database, we performed a series of replication analyses demonstrating some common analyses conducted in retrospective observational research with complex EHR-derived data to generate evidence. Eligible patients were selected into biomarker- and treatment-defined cohorts, first with expert-abstracted then with ML-extracted data. We utilized the biomarker- and treatment-defined cohorts to perform analyses related to biomarker-associated survival and treatment comparative effectiveness, respectively. Across all analyses, the results differed by less than 8% between the data curation methods, and similar conclusions were reached. These results highlight that high-performance ML-extracted variables trained on expert-abstracted data can achieve similar results as when using abstracted data, unlocking the ability to perform oncology research at scale.
Isolation and NMR Scaling Factors for the Structure Determination of Lobatolide H, a Flexible Sesquiterpene from Neurolaena lobata

A new flexible germacranolide (1, lobatolide H) was isolated from the aerial parts of Neurolaena lobata. The structure elucidation was performed by classical NMR experiments and DFT NMR calculations. Altogether, 80 theoretical level combinations with existing 13C NMR scaling factors were tested, and the best performing ones were applied on 1. 1H and 13C NMR scaling factors were also developed for two combinations utilizing known exomethylene containing derivatives, and the results were complemented by homonuclear coupling constant (JHH) and TDDFT-ECD calculations to elucidate the stereochemistry of 1. Lobatolide H possessed remarkable antiproliferative activity against human cervical tumor cell lines with different HPV status (SiHa and C33A), induced cell cycle disturbance and exhibited a substantial antimigratory effect in SiHa cells.
Predicting successful and unsuccessful transitions from school to work by using sequence methods

Policy makers recognize the importance of identifying early young people who are likely to end up jobless on entry to the adult labour market. This paper uses sequence techniques to characterize 712 young peoples' transitions from school to work into `types', with jobless types interpreted as unsuccessful transitions. A logit model is estimated for transition type using a collection of static individual, family and school characteristics. This allows us to identify which young people are most likely to experience unsuccessful transitions into the adult labour market. Policy makers might use such information to target social and educational policy more effectively to promote social inclusion.
Omnidimensional Convex Polytopes

The study shows that the volumes and surfaces of n-balls, n-simplices, and n-orthoplices are holomorphic functions of n, which makes those objects omnidimensional, that is well defined in any complex dimension. Applications of these formulas to the omnidimensional polytopes inscribed in and circumscribed about n-balls reveal previously unknown properties of these geometric objects. In particular, for 0<n<1, the volumes of the omnidimensional polytopes are larger than those of circumscribing n-balls, and both their volumes and surfaces are smaller than those of inscribed n-balls. The surface of an n-simplex circumscribing a unit diameter n-ball is spirally convergent to zero with real n approaching negative infinity but first has a local maximum at n=−3.5. The surface of an n-orthoplex circumscribing a unit diameter n-ball is spirally divergent with real n approaching negative infinity but first has a local minimum at n=−1.5, where its real and imaginary parts are equal to each other; similarly, is its volume, where the similar local minimum occurs at n=−3.5. Reflection functions for volumes and surfaces of these polytopes inscribed in and circumscribed about n-balls are proposed. Symmetries of products and quotients of the volumes in complex dimensions n and −n and of the surfaces in complex dimensions n and 2−n are shown to be independent of the metric factor and the gamma function. Specific symmetries also hold between the volumes and surfaces in dimensions n=−1/2 and n=1/2.
Benchmark Tool for Detecting Anomalous Program Behaviour on Embedded Devices

This paper presents an open-source benchmark tool for anomaly detection in program behaviour, using program counter (PC) and instruction type information. It is introducing anomalies in artificial way, allowing for fine-grained evaluation with adjustable sliding window sizes and preprocessing configuration. The usage of the benchmark, including demonstrated data collection, does not require any additional hardware other than a standard computer. The benchmark uses the output of llvm-objdump program to focus on non-library code which allows for rapid evaluation of various detection methods with different configurations. The proposed tool extracts features derived from processor’s PC and instruction type information and then utilizes the features to identify abnormal behavior using 4 different anomaly detection algorithms. New detection methods can be easily incorporated into the benchmark, which provides a solid foundation for evaluating novel, previously unseen methods against methods we selected for our experiment.
Evaluation of Parity Effect on Characteristics and Minerals in Buffalo (Bubalus Bubalis) Colostrum and Mature Milk

Colostrum is a vital performance for buffaloes and potentially functional foods in the future. Therefore, this study aimed to evaluate the difference between the parity of buffalo colostrum and mature milk. Twenty pregnant buffaloes (primiparous = 10; multiparous = 10) were assigned to the same diet prepartum and milking routine postpartum. Calves were separated from the dams immediately after birth and colostrum was harvested within 2 h, whilst mature milk was harvested at 7 days postpartum. The colostrum was analyzed for immunoglobulin G and milk composition as the mature milk. The results showed that there was a higher level of protein, solid not fat, and milk urea nitrogen (p < 0.05), with a tendency for higher total solids (p = 0.08) in primiparous buffaloes’ colostrum compared with multiparous. No parity effect was observed in colostrum immunoglobulin G, fat, lactose, and yields of colostrum and composition (p > 0.05). There was no difference in mature milk composition and yield by parity affected (p > 0.05). Compared with mature milk composition, colostrum had a higher content protein, total solids, solid not fat, and milk urea nitrogen (p < 0.05); however, fat and lactose were lower than that of mature milk (p < 0.05). For minerals, multiparous buffaloes’ colostrum had a higher concentration of Fe (p = 0.05), while the mature milk had higher concentrations of K and P compared with primiparous. Buffalo colostrum had higher concentrations of Na, Mg, Co, Fe, and K with a lower concentration of Ca relative to mature milk (p < 0.05). It was observed that parity affected colostrum characteristics rather than mature milk and caused subtle variations in minerals in colostrum and mature milk of buffaloes. As lactation proceeded, both milk composition and minerals in the milk changed drastically.
Association of Diabetes Mellitus with All-Cause and Cause-Specific Mortality among Patients with Metabolic-Dysfunction-Associated Fatty Liver Disease: A Longitudinal Cohort Study

Background: Diabetes mellitus (DM) is a comorbidity commonly presenting with metabolic-dysfunction-associated fatty liver disease (MAFLD); however, few tests for interaction have been reported. Our target was to evaluate the prognostic implications of DM in patients with different forms of MAFLD. Methods: Using data from the Third National Health and Nutrition Examination Survey (NHANES III) in the United States, we screened 14,797 participants aged 20–74 who received ultrasound examinations from 1988–1994. Among them, 4599 patients met the diagnosis of MAFLD, and we defined mortality as the outcome event. Survival analysis of competitive risk events was performed using Cox regression and sub-distributed risk ratio (SHR). Results: During 21.1 years of follow-up, cardiovascular diseases seemed to be the most common cause of death among MAFLD patients. Of them, DM was present in 25.48% and was independently associated with increased risk of all-cause mortality (HRs: 1.427, 95% CIs: 1.256–1.621, p < 0.001) and cause-specific mortality (cardiovascular-related mortality (HRs: 1.458, 95% CIs: 1.117–1.902, p = 0.005), non-cardiovascular-related mortality (HRs: 1.423, 95% CIs: 1.229–1.647, p < 0.001), and non-cancer-related mortality (HRs: 1.584, 95% CIs: 1.368–1.835, p < 0.001), respectively). Surprisingly, this association was more significant for young patients (p-value for interaction <0.001). Moreover, DM had a greater risk of all-cause and cause-specific mortality among overweight and obese MAFLD patients (p-value for interaction <0.001). Conclusions: DM increased the risk of all-cause and cause-specific mortality (cardiovascular-related, non-cardiovascular-related, and non-cancer-related) in MAFLD patients, especially in younger patients with excess obesity.
The Evolution of a Self-Sustained Oscillation in a Nonlinear Continuous System

Abstract : A gas filled tube has a pressure sensitive heat source at the center, while energy is allowed to radiate from the ends. For a sufficiently large feedback coefficient the system is linearly unstable. Within the nonlinear theory, the self-excited oscillation initially grows until a shock forms. The shock acts as a dissipative mechanism so that a balance is achieved and ultimately a time periodic state is reached. The small amplitude disturbance in the pipe is represented as the superposition of two simple waves traveling in opposite directions, and without interaction. Based on this representation the problem reduces to solving a nonlinear difference equation. (Author)
Ablation of GPR56 Causes β-Cell Dysfunction by ATP Loss through Mistargeting of Mitochondrial VDAC1 to the Plasma Membrane

The activation of G Protein-Coupled Receptor 56 (GPR56), also referred to as Adhesion G-Protein-Coupled Ceceptor G1 (ADGRG1), by Collagen Type III (Coll III) prompts cell growth, proliferation, and survival, among other attributes. We investigated the signaling cascades mediating this functional effect in relation to the mitochondrial outer membrane voltage-dependent anion Channel-1 (VDAC1) expression in pancreatic β-cells. GPR56KD attenuated the Coll III-induced suppression of P70S6K, JNK, AKT, NFκB, STAT3, and STAT5 phosphorylation/activity in INS-1 cells cultured at 20 mM glucose (glucotoxicity) for 72 h. GPR56-KD also increased Chrebp, Txnip, and Vdac1 while decreasing Vdac2 mRNA expression. In GPR56-KD islet β-cells, Vdac1 was co-localized with SNAP-25, demonstrating its plasma membrane translocation. This resulted in ATP loss, reduced cAMP production and impaired glucose-stimulated insulin secretion (GSIS) in INS-1 and human EndoC βH1 cells. The latter defects were reversed by an acute inhibition of VDAC1 with an antibody or the VDAC1 inhibitor VBIT-4. We demonstrate that Coll III potentiates GSIS by increasing cAMP and preserving β-cell functionality under glucotoxic conditions in a GPR56-dependent manner by attenuating the inflammatory response. These results emphasize GPR56 and VDAC1 as drug targets in conditions with impaired β-cell function.
Thoracolumbar Scoliosis in Pediatric Patients With Loeys-Dietz Syndrome: A Case Series

Background Loeys-Dietz syndrome (LDS) is a genetic connective tissue disorder that predominantly affects cardiovascular, skeletal, and craniofacial structures. Associated thoracolumbar scoliosis in LDS can be challenging to manage, though other etiologies of pediatric scoliosis have better-defined management guidelines. We examined our institutional experience regarding the treatment of pediatric patients with LDS and scoliosis. Methodology In this retrospective study, all patients seen at our pediatric tertiary care center from 2004 through 2018 with a diagnosis of LDS were reviewed, and those with radiographic diagnoses of scoliosis (full-length scoliosis X-rays) were included. Demographic, clinical, and radiographic parameters were collected, and management strategies were reported. Results A total of 39 LDS patients whose ages ranged between seven and 13 years were identified. A total of nine patients were radiographically diagnosed with scoliosis, but three patients were excluded due to incomplete medical records, leaving six patients. The median age at scoliosis diagnosis was 11.5 years, with a median follow-up of 51 months. Two patients were successfully managed with observation (average initial Cobb angle (CA): 14°, average final CA: 20.5°). Two were braced, one successfully (initial CA: 15°, final CA: 30°) and one with a progressive disease requiring surgery (initial CA: 40°, final CA: 58°). Of the two who were offered surgical correction, one underwent surgery with a durable correction of spinal deformity (CA: 33° to 19°). One patient underwent a recent correction of aortic root dilatation and was not a candidate for scoliosis surgery. Conclusions Principles of adolescent idiopathic scoliosis management such as bracing for CA of 20-50° and surgery for CA of >50° can be applied to LDS patients with good outcomes. This augments our understanding of the treatment algorithm for pediatric patients with LDS.
Accuracy of Partial Coherence Interferometry in Intraocular Lens Power Calculation

Purpose: To evaluate the accuracy and the influencing factors of partial coherence interferometry in intraocular lens (IOL) power calculation for cataract surgery. Methods: In 86 eyes of 69 patients who had undergone cataract surgery, we measured axial length using both IOLMaster and contact type ultrasonography, calculated the target refraction with SRK II formula and compared the result with the measured value after operation. We also evaluated the factors influencing the accuracy of the power calculation such as age, sex, type of cataract, severity of nucleosclerosis, corneal power, and preoperative refraction. Results: In IOLMaster and contact type ultrasonography, the mean axial lengths were 23.701. 27 mm and 23.551. 28 mm (p0.26D and 0.660. 39D (p
Open Reading Frame 4 Is Not Essential in the Replication and Infection of Genotype 1 Hepatitis E Virus

Genotype 1 hepatitis E virus (HEV-1), unlike other genotypes of HEV, has a unique small open reading frame known as ORF4 whose function is not yet known. ORF4 is located in an out-framed manner in the middle of ORF1, which encodes putative 90 to 158 amino acids depending on the strains. To explore the role of ORF4 in HEV-1 replication and infection, we cloned the complete genome of wild-type HEV-1 downstream of a T7 RNA polymerase promoter, and the following ORF4 mutant constructs were prepared: the first construct had TTG instead of the initiation codon ATG (A2836T), introducing an M→L mutation in ORF4 and a D→V mutation in ORF1. The second construct had ACG instead of the ATG codon (T2837C), introducing an M→T mutation in ORF4. The third construct had ACG instead of the second in-frame ATG codon (T2885C), introducing an M→T mutation in ORF4. The fourth construct contained two mutations (T2837C and T2885C) accompanying two M→T mutations in ORF4. For the latter three constructs, the accompanied mutations introduced in ORF1 were all synonymous changes. The capped entire genomic RNAs were generated by in vitro transcription and used to transfect PLC/PRF/5 cells. Three mRNAs containing synonymous mutations in ORF1, i.e., T2837CRNA, T2885CRNA, and T2837C/T2885CRNA, replicated normally in PLC/PRF/5 cells and generated infectious viruses that successfully infected Mongolian gerbils as the wild-type HEV-1 did. In contrast, the mutant RNA, i.e., A2836TRNA, accompanying an amino acid change (D937V) in ORF1 generated infectious viruses upon transfection, but they replicated slower than the wild-type HEV-1 and failed to infect Mongolian gerbils. No putative viral protein(s) derived from ORF4 were detected in the wild-type HEV-1- as well as the mutant virus-infected PLC/PRF/5 cells by Western blot analysis using a high-titer anti-HEV-1 IgG antibody. These results demonstrated that the ORF4-defective HEV-1s had the ability to replicate in the cultured cells, and that these defective viruses had the ability to infect Mongolian gerbils unless the overlapping ORF1 was accompanied by non-synonymous mutation(s), confirming that ORF4 is not essential in the replication and infection of HEV-1.
Phase Transition and Slowing Down in Non-Equilibrium Stochastic Processes

A general criterion of appearance of slowing down in non·equilibrium stochastic processes is proposed. Many examples for this general criterion are shown, in which a phenomenon of slowing down occurs at a certain value of the relevant parameter. In particular, a generalized scaling treatment of transient phenomena is effectively applied to deriving the relaxation spectra of some multiplicative stochastic processes. The concept of asymptotic slowing down for finite systems is also proposed.
A Review on Strategies for Hybrid DC/AC Microgrid Power Management

Microgrids are integrated electricity systems that are relatively compact. The microgrid is a cluster of distributed generators, an energy storage system with a controllable load. The Power management, as well as stability of hybrid DC/ AC microgrid, are discussed in detail in this work. While the stand-alone operation is a crucial aspect of microgrids, their full potential will not be achieved until grid connection and a smooth transition are implemented. This work attempts to address some of the many questions that remain about these operation modes. Given that it is closely related to the other operating states of the microgrid, the standalone mode has been changed. The conditions for connecting microgrids to the main grid are examined. Comparing hybrid DC/AC microgrids to other microgrid topologies reveals that they have more benefits in terms of efficiency and economy.