Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome

Microbial community varied from one site to another along the gastrointestinal tract, but current studies about intestinal microbial community in IBS-D were mainly based on fecal samples. Based on 283 intestinal samples collected from DM, DL, RM, and RL of HC and IBS-D, we found different intestinal sites had their site-specific microbial patterns in IBS-D. ABSTRACT Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites. This study recruited 74 IBS-D patients and 20 healthy controls (HC). 22.34%, 8.51%, 14.89%, and 54.26% of them contributed to one, two, three, and four sites: duodenal mucosa (DM), duodenal lumen (DL), rectal mucosa (RM), and rectal lumen (RL) of intestinal samples, respectively. Then 16S rRNA gene analysis was performed on these 283 samples. The result showed that IBS-D microbial communities have specific patterns at each intestinal site differing from that of HC. Across hosts and sites, Bacillus, Burkholderia, and Faecalibacterium were the representative genera in duodenum of IBS-D, duodenum of HC, and rectum of HC, respectively. Samples from mucosa and lumen in rectum were highly distinguishable, regardless of IBS-D and HC. Additionally, IBS-D patients have lower microbial co-abundance network connectivity. Moreover, RM site-specific biomarker: Bacteroides used alone or together with Prevotella and Oscillospira in RM showed outstanding performance in IBS-D diagnosis. Furthermore, Bacteroides and Prevotella in RM were strongly related to the severity of abdominal pain, abdominal discomfort, and bloating in IBS-D patients. In summary, this study also confirmed fecal microbial community could not fully characterize intestinal microbial communities. Among these site-specific microbial communities, RM microbial community would be more applicable in the diagnosis of IBS-D. IMPORTANCE Microbial community varied from one site to another along the gastrointestinal tract, but current studies about intestinal microbial community in IBS-D were mainly based on fecal samples. Based on 283 intestinal samples collected from DM, DL, RM, and RL of HC and IBS-D, we found different intestinal sites had their site-specific microbial patterns in IBS-D. Notably, RM site-specific microbes Bacteroides, Prevotella, and Oscillospira could be used to discriminate IBS-D from HC accurately. Our findings could help clinicians realize the great potential of the intestinal microbial community in RM for better diagnosis of IBS-D patients.
Two Cholesterol Recognition Amino Acid Consensus Motifs of GP64 with Uncleaved Signal Peptide Are Required for Bombyx mori Nucleopolyhedrovirus Infection

BmNPV is a severe pathogen that mainly infects silkworms. GP64 is the key membrane fusion protein that mediates BmNPV infection, and some studies have indicated that cholesterol and lipids are involved in BmNPV infection. ABSTRACT The signal peptide (SP) of integrated membrane proteins is removed cotranslationally or posttranslationally in the endoplasmic reticulum, while GP64, a membrane fusion protein of Bombyx mori nucleopolyhedrovirus (BmNPV), retains its SP in the mature protein and virion. In this study, we revealed that uncleaved SP is a key determinant with additional functions in infection. First, uncleaved SP endows BmNPV with strong virulence; second, SP retention-induced BmNPV infection depends on cholesterol recognition amino acid consensus domain 1 (CRAC1) and CRAC2. In contrast, the recombinant virus with SP-cleaved GP64 has reduced infectivity, and only CRAC2 is required for BmNPV infection. Furthermore, we showed that cholesterol in the plasma membrane is an important fusion receptor that interacts with CRAC2 of GP64. Our study suggested that BmNPV GP64 is a key cholesterol-binding protein and uncleaved SP determines GP64's unique dependence on the CRAC domains. IMPORTANCE BmNPV is a severe pathogen that mainly infects silkworms. GP64 is the key membrane fusion protein that mediates BmNPV infection, and some studies have indicated that cholesterol and lipids are involved in BmNPV infection. A remarkable difference from other membrane fusion proteins is that BmNPV GP64 retains its SP in the mature protein, but the cause is still unclear. In this study, we investigated the reason why BmNPV retains this SP, and its effects on protein targeting, virulence, and CRAC dependence were revealed by comparison of recombinant viruses harboring SP-cleaved or uncleaved GP64. Our study provides a basis for understanding the dependence of BmNPV infection on cholesterol/lipids and host specificity.
A REDUCED-RANKAPPROACHTO ADAPTIVE LINEARLY CONSTRAINEDMINIMUM VARIANCEBEAMFORMINGBASED ON JOINT ITERATIVE OPTIMIZATIONOF ADAPTIVE FILTERS

This paper presents a low-complexity reduced-rank approach to adaptive linearly constrained minimum variance (LCMV) beam­ forming. The proposed reduced-rank scheme is based on a con­ strained joint iterative optimization of adaptive filters according to the minimum variance criterion. The constrained joint iter­ ative optimization procedure adjusts the parameters of a bank of full-rank adaptive filters that forms the projection matrix and an adaptive reduced-rank filter that operates at the output of the bank of filters. We describe LCMV expressions for the design of the projection matrix and the reduced-rank filter and low­ complexity stochastic gradient adaptive algorithms for their ef­ ficient implementation. Simulations for a beamforming applica­ tion show that the proposed scheme outperforms in convergence and tracking the state-of-the-art existing reduced-rank schemes with significantly lower complexity.
Functional Genomics and Comparative Lineage-Specific Region Analyses Reveal Novel Insights into Race Divergence in Verticillium dahliae

Deciphering the gene-for-gene relationships during host-pathogen interactions is the basis of modern plant resistance breeding. In the Verticillium dahliae-tomato pathosystem, two races (races 1 and 2) and their corresponding avirulence (Avr) genes have been identified, but strains that lacked these two Avr genes exist in nature. ABSTRACT Verticillium dahliae is a widespread soilborne fungus that causes Verticillium wilt on numerous economically important plant species. In tomato, until now, three races have been characterized based on the response of differential cultivars to V. dahliae, but the genetic basis of race divergence in V. dahliae remains undetermined. To investigate the genetic basis of race divergence, we sequenced the genomes of two race 2 strains and four race 3 strains for comparative analyses with two known race 1 genomes. The genetic basis of race divergence was described by the pathogenicity-related genes among the three races, orthologue analyses, and genomic structural variations. Global comparative genomics showed that chromosomal rearrangements are not the only source of race divergence and that race 3 should be split into two genotypes based on orthologue clustering. Lineage-specific regions (LSRs), frequently observed between genomes of the three races, encode several predicted secreted proteins that potentially function as suppressors of immunity triggered by known effectors. These likely contribute to the virulence of the three races. Two genes in particular that can act as markers for race 2 and race 3 (VdR2e and VdR3e, respectively) contribute to virulence on tomato, and the latter acts as an avirulence factor of race 3. We elucidated the genetic basis of race divergence through global comparative genomics and identified secreted proteins in LSRs that could potentially play critical roles in the differential virulence among the races in V. dahliae. IMPORTANCE Deciphering the gene-for-gene relationships during host-pathogen interactions is the basis of modern plant resistance breeding. In the Verticillium dahliae-tomato pathosystem, two races (races 1 and 2) and their corresponding avirulence (Avr) genes have been identified, but strains that lack these two Avr genes exist in nature. In this system, race 3 has been described, but the corresponding Avr gene has not been identified. We de novo-sequenced genomes of six strains and identified secreted proteins within the lineage-specific regions (LSRs) distributed among the genomes of the three races that could potentially function as manipulators of host immunity. One of the LSR genes, VdR3e, was confirmed as the Avr gene for race 3. The results indicate that differences in transcriptional regulation may contribute to race differentiation. This is the first study to describe these differences and elucidate roles of secreted proteins in LSRs that play roles in race differentiation.
A new instantaneous torque control of PM synchronous motor for high performance direct drive applications

A new instantaneous torque control strategy is presented for the high performance control of a permanent magnet synchronous motor. In order to deal with the torque pulsation problem of the PM synchronous motor in the low-speed region, new torque estimation and control techniques are proposed. The linkage flux of the PM synchronous motor is estimated using a model reference adaptive control system technique and the developed torque of the motor is instantaneously controlled by a torque controller combining variable structure control with space vector PWM. The proposed control scheme provides the advantage of reducing the torque pulsation caused by the nonsinusoidal flux distribution of the motor. This control strategy is applied to a high torque PM synchronous motor drive system for direct drive applications and implemented by using a software of the DSP TMS320C30. Computer simulations and experiments are carried out for this system and the results demonstrate well the effectiveness of the proposed control strategy.
Consensus guidelines for antifungal prophylaxis in haematological malignancy and haemopoietic stem cell transplantation, 2021

Antifungal prophylaxis can reduce morbidity and mortality from invasive fungal disease (IFD). However, its use needs to be optimised and appropriately targeted to patients at highest risk to derive the most benefit. In addition to established risks for IFD, considerable recent progress in the treatment of malignancies has resulted in the development of new ‘at‐risk’ groups. The changing epidemiology of IFD and emergence of drug resistance continue to impact choice of prophylaxis, highlighting the importance of active surveillance and knowledge of local epidemiology. These guidelines aim to highlight emerging risk groups and review the evidence and limitations around new formulations of established agents and new antifungal drugs. It provides recommendations around use and choice of antifungal prophylaxis, discusses the potential impact of the changing epidemiology of IFD and emergence of drug resistance, and future directions for risk stratification to assist optimal management of highly vulnerable patients.
Artificial Intelligence Based Myocardial Ischemia Detection in Cardiac Radiology

Artifical intelligence (AI) is changing many aspects of our lives. It includes machine learning (ML) and deep learning (DL), which can automatically obtain information from the database through algorithms and make predictions. It has been widely used in medicine, especially in the cardiovascular field. In this review, we made a brief overview of AI, as well as the application of AI in the cardiac radiology to noninvasively detect myocardial ischemia. At the same time, we summarized the current limitations and prospects of AI in the field of myocardial ischemia. Finally, AI can accomplish the task of image recognition very well, and make accurate judgments with the same effectiveness as cardiologists or imaging experts.
Oblique instability of a stratified oscillatory boundary layer

Abstract The instability and dynamics of a vertical oscillatory boundary layer in a container filled with a stratified fluid are addressed. Past experiments have shown that when the boundary oscillation frequency is of the same order as the buoyancy frequency, the system is unstable to a herringbone pattern of oblique waves. Prior studies assuming the basic state to be a unidirectional oscillatory shear flow were unable to account for the oblique waves. By accounting for confinement effects present in the experiments, and the ensuing three-dimensional structure of the basic state, we are able to numerically reproduce the experimental observations, opening the door to fully analysing the impacts of stratification on such boundary layers.
Calibrating Water Distribution Network Models

Calibration of water distribution network models is necessary in predicting their behavior under different loading conditions or in planning their expansions. Of the several data used in calibration, the predicted nodal demands and the pipe resistance coefficients are the least reliable. The model user usually adjusts the pipe resistance coefficients and/or the nodal demands by trial‐and‐error procedure and achieves calibration by making the predicted nodal pressures reasonably agree with the observed nodal pressures. A systematic iterative calibration procedure that decides the required adjustments in the nodal demands and pipe resistance coefficients is developed in this paper. The procedure is also illustrated through an example network.
Survey of Optical Environment over Hemisphere-on- Cylinder Turret Using Suite of Wavefront Sensors

Extensive measurements of the optical environment around a generic hemisphere-oncylinder turret with a conformal window were performed for both forwardand backwardlooking elevation angles using a Malley probe, conventional 2-D wavefront sensor and highbandwidth 8x8 wavefront sensor for a range of Mach numbers from 0.35 to 0.45. A necklace vortex at the bottom of the turret and the shear layer structures formed in the separated region of the flow were identified as the main causes of optical distortions imposed on a laser beam. Different instruments provide different, but complimentary information about the aberrating structures. The Malley probe data can distinguish between stationary and traveling aberrations, but provides 1-D slices of wavefronts only, while the 2-D wavefront sensor data gives time-uncorrelated sets of highly spatially resolved wavefronts. The highbandwidth, 8x8 wavefront sensor data provides a unique opportunity to decompose wavefronts into their stationary and convective components. Oil-flow visualization revealed a complex topology of the flow around the turret.
dnaJ: a New Approach to Identify Species within the Genus Enterobacter

We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF. ABSTRACT The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI). We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type-strain library and the SeqScape software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research. IMPORTANCE We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF.
FIR system identification via second-order statistics

In many practical applications, it is of interest to identify unknown system characteristics so as to recover input source signals from the observed data. In this paper, we specially consider a model with two receivers, and the outputs are described by FIR equations. Our approach involves the estimation of the FIR coefficients and the construction of the input signals by second-order statistics, i.e. the use of the auto-power and crosspower spectra of the two receiver signals. To accommodate time-varying situations and to serve online purposes, a recursive weighted least squares algorithm is proposed. Comparing with other higher-order statistics approaches, our method is not restricted to independent and identically distributed (i.i.d.) random signals and has less computation burden. Our simulation results also show that the performance of our algorithm is comparable to Giannakis's third-order statistics approach.
Diagnostic Monitoring Of Vigilance Decrement Using EEG Workload Indices

The resource model of vigilance (Warm, Parasuraman, & Matthews, 2008) suggests that EEG-based indices of workload might be used to monitor the operator’s fitness to sustain signal detection. 92 participants performed a 40 minute vigilance task believed to be sensitive to resource availability. Half performed in a cued condition, half without cues. Findings confirmed that cueing reduces workload and enhances vigilance. EEG was recorded throughout performance. Of the various EEG indices analyzed, lower frequency alpha and the Task Load Index (TLI) corresponded most closely to changes in signal detection rates. Other indices, the Engagement Index (EI) and frontal theta, did not show systematic decrement but discriminated cued and uncued conditions towards the end of the task. Implications of the findings for using EEG to drive adaptive automation are discussed.
A universal velocity profile for turbulent wall flows including adverse pressure gradient boundary layers

Abstract A recently developed mixing length model of the turbulent shear stress in pipe flow is used to solve the streamwise momentum equation for fully developed channel flow. The solution for the velocity profile takes the form of an integral that is uniformly valid from the wall to the channel centreline at all Reynolds numbers from zero to infinity. The universal velocity profile accurately approximates channel flow direct numerical simulation (DNS) data taken from several sources. The universal velocity profile also provides a remarkably accurate fit to simulated and experimental flat plate turbulent boundary layer data including zero and adverse pressure gradient data. The mixing length model has five free parameters that are selected through an optimization process to provide an accurate fit to data in the range $R_\tau = 550$ to $R_\tau = 17\,207$. Because the velocity profile is directly related to the Reynolds shear stress, certain statistical properties of the flow can be studied such as turbulent kinetic energy production. The examples presented here include numerically simulated channel flow data from $R_\tau = 550$ to $R_\tau =8016$, zero pressure gradient (ZPG) boundary layer simulations from $R_\tau =1343$ to $R_\tau = 2571$, zero pressure gradient turbulent boundary layer experimental data between $R_\tau = 2109$ and $R_\tau = 17\,207$, and adverse pressure gradient boundary layer data in the range $R_\tau = 912$ to $R_\tau = 3587$. An important finding is that the model parameters that characterize the near-wall flow do not depend on the pressure gradient. It is suggested that the new velocity profile provides a useful replacement for the classical wall-wake formulation.
Above 2000 V breakdown voltage at 600 K GaN‐on‐silicon high electron mobility transistors

We report a three‐terminal breakdown voltage over 3 kV on AlGaN/GaN high electron mobility transistors (HEMTs) grown on 6‐in. silicon (111) substrate with a buffer thickness of 5.5 μm. A local substrate removal all around the drain of the transistors has been developed in order to suppress the parasitic substrate conduction, which enables improving the device breakdown voltage by more than 200%. This establishes a new record breakdown voltage for GaN‐on‐silicon lateral power devices while maintaining a low‐specific on‐resistance of about 10 m Ω cm2. Furthermore, the device performance has been investigated at elevated temperature up to 600 K under high vacuum. Breakdown voltages well above 2 kV at temperatures exceeding 300 °C have been achieved for the first time owing to the suppression of the buffer layer/Silicon substrate parasitic conduction. These data demonstrates that the local substrate removal is not only an efficient solution to significantly boost the device breakdown voltage but also allows improving the high voltage operation under high temperature, which is a key feature for high power electronic applications.
Add-drop multiplexing by dispersion inverted interference coupling

We demonstrate experimentally a previously proposed add-drop multiplexer in a two-moded structure with a symmetric Bragg grating. The strong dispersion in the forward direction outside the reflective region of the grating is used to create a phase change for frequencies between the bandgaps of the supermodes of a twin core fiber. The phase change in transmission inverts the interference pattern at the end of the device. Signals within a narrow wavelength range couple out to one core; all other wavelengths couple out to the opposite core. Preliminary experimental results show a crosstalk ratio of 15 dB.
Clinical Trials of Oncolytic Viruses in Breast Cancer

Breast cancer is the second most common kind of cancer worldwide and oncolytic viruses may offer a new treatment approach. There are three different types of oncolytic viruses used in clinical trials; (i) oncolytic viruses with natural anti-neoplastic properties; (ii) oncolytic viruses designed for tumor-selective replication; (iii) oncolytic viruses modified to activate the immune system. Currently, fourteen different oncolytic viruses have been investigated in eighteen published clinical trials. These trials demonstrate that oncolytic viruses are well tolerated and safe for use in patients and display clinical activity. However, these trials mainly studied a small number of patients with different advanced tumors including some with breast cancer. Future trials should focus on breast cancer and investigate optimal routes of administration, occurrence of neutralizing antibodies, viral gene expression, combinations with other antineoplastic therapies, and identify subtypes that are particularly suitable for oncolytic virotherapy.