Miracle-dz/UniFAR-FTUs huggingface dataset:
A convenient strategy to clone small RNA and mRNA for high-throughput sequencing

High-throughput sequencing has become a standard tool for analyzing RNA and DNA. This method usually needs a cDNA/DNA library ligated with specific 5′ and 3′ linkers. Unlike mRNA, small RNA often contains modifications including 5′ cap or triphosphate and 2′-O-methyl, requiring additional processing steps before linker additions during cloning processes; due to low expression levels, it is difficult to clone small RNA with a small amount of total RNA. Here we present a new strategy to clone 5′ modified or unmodified small RNA in an all-liquid-based reaction carried out in a single PCR tube with as little as 20 ng total RNA. The 7-h cloning process only needs ∼1 h of labor. Moreover, this method can also clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA; the barcoded PCR primers are also compatible with non-cDNA cloning applications, including the preparation of genomic libraries. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, versatile, and cost-effective. Moreover, the all-liquid-based reaction can be performed in an automated manner.
Overbinding, qualitative and quantitative changes caused by simple Na+ and K+ ions in polyelectrolyte simulations: comparison of force fields with and without NBFIX and ECC corrections.

Overbinding of ions is a common and well-known problem in classical molecular dynamics (MD) simulations. One of its main causes is the absence of electronic polarizability in the force fields. The current approaches for minimizing overbinding typically either retain the original charges and use an ad hoc re-adjustment of the Lennard-Jones parameters as done in the non-bonded fix (NBFIX) approach or re-scaling of charges using a theoretical framework. The goal in the latter is to include shielding produced by the missing electronic polarizability as done in the electronic continuum correction (ECC) approach. NBFIX and ECC are the most common corrections and we compare their performance to the default parameterizations provided by five different commonly used biomolecular force fields, OPLS-AA/L, CHARMM27, CHARMM36m, CHARMM22* and AMBER99SB-ILDN. As test systems, we use poly-α,L-glutamic (PGA) and poly-α,L-aspartic (PASA) amino acids molecules in explicit water together with Na+ and K+ counterions. We demonstrate that the different force fields yield results that are not only quantitatively but also qualitatively different. The resulting structures of the macroions depend strongly on the model for ions. NBFIX corrections alleviate the problem of overbinding, resulting in extended peptides. The ECC corrections depend non-trivially on the original underlying model and despite being based on a theoretical framework, cannot always solve the problem.
Global Transcriptional Analysis of Nontransformed Human Intestinal Epithelial Cells (FHs 74 Int) after Exposure to Selected Drinking Water Disinfection By-Products

Background: Drinking water disinfection inadvertently leads to the formation of numerous disinfection by-products (DBPs), some of which are cytotoxic, mutagenic, genotoxic, teratogenic, and potential carcinogens both in vitro and in vivo. Objectives: We investigated alterations to global gene expression (GE) in nontransformed human small intestine epithelial cells (FHs 74 Int) after exposure to six brominated and two chlorinated DBPs: bromoacetic acid (BAA), bromoacetonitrile (BAN), 2,6-dibromo-p-benzoquinone (DBBQ), bromoacetamide (BAM), tribromoacetaldehyde (TBAL), bromate (BrO3−), trichloroacetic acid (TCAA), and trichloroacetaldehyde (TCAL). Methods: Using whole-genome cDNA microarray technology (Illumina), we examined GE in nontransformed human cells after 4h exposure to DBPs at predetermined equipotent concentrations, identified significant changes in gene expression (p≤0.01), and investigated the relevance of these genes to specific toxicity pathways via gene and pathway enrichment analysis. Results: Genes related to activation of oxidative stress–responsive pathways exhibited fewer alterations than expected based on prior work, whereas all DBPs induced notable effects on transcription of genes related to immunity and inflammation. Discussion: Our results suggest that alterations to genes associated with immune and inflammatory pathways play an important role in the potential adverse health effects of exposure to DBPs. The interrelationship between these pathways and the production of reactive oxygen species (ROS) may explain the common occurrence of oxidative stress in other studies exploring DBP toxicity. Finally, transcriptional changes and shared induction of toxicity pathways observed for all DBPs caution of additive effects of mixtures and suggest further assessment of adverse health effects of mixtures is warranted. https://doi.org/10.1289/EHP4945
Influence of Different Methionine Sources on Performance and Slaughter Characteristics of Broilers

Simple Summary The increasing public demand for efficient, sustainably produced poultry meat with simultaneous optimization of animal welfare is calling for amendments in meat production. A starting point to meet this demand consists of complete diets for broilers with reduced crude protein content, supplemented with higher amounts of crystalline amino acids. This ensures sufficient nutritional supply and decreased nitrogen excretion for environmental relief. To optimize the performance and health, despite the drastically reduced protein content (~17.5% finisher diet), the present study compared different methionine sources (methionine hydroxy analog, DL-methionine, and L-methionine) in slightly higher dosages than found in practice, in comparison to a diet meeting the methionine requirements using methionine hydroxy analog. Methionine is the first limiting amino acid and has a significant influence on the health and growth of the animals. The results of the feeding trial showed no differences concerning general health, ileal histology, and performance data of broilers before slaughter. However, the composition of the breast meat differed significantly (highest protein content and lowest fat content in the L-methionine group), and thus provides the impetus for further research. Abstract Sustainably produced poultry meat with consideration of animal health poses a challenge for broiler production. Low protein diets with high amounts of synthetic amino acids (AAs) like methionine (Met) are the consequence. In a five-week feeding trial, 360 broilers (Ross 308) assigned to four feeding groups were offered protein-reduced complete diets (starter: 20% crude protein (CP); grower: 18.5% CP; finisher: 17.5% CP), supplemented with essential AAs. The “MHA” group received DL-2-hydroxy-4-(methylthio) butanoic acid (DL-HMTBA; trade name: MHA®), groups “L” and “DL” the respective Met source in equivalent concentrations each exceeding the nutritional recommendations. “R-MHA” (“R” for “reduced”) received the minimum required level (using MHA as Met source). Performance exceeded performance goals without differences between the groups. The average feed conversion ratio (FCR) amounted to 1.35. The carcass/body weight ratio of R-MHA was significantly lower (0.782) compared to DL (0.808) and L (0.809). Breast meat of R-MHA contained significantly more fat (144 g/kg dry matter (DM)) compared to L (104 g/kg DM) and significantly lower CP content (R-MHA: 838 g/kg DM; L: 875 g/kg DM). The results indicated possible improvement in slaughter yield by protein-reduced diets supplemented with L-Met, thus recommending further research focusing on the Met influence.
Adaptive Lane Keeping Assistance System design based on driver’s behavior

The lane keeping assistance system can reduce the risk of lane departure effetely, but the control parameters in the existing system are fixed and single warning algorithm is hard to adapt to different drivers. And the decision-making logic for lane keeping intervention is relatively simple, and cannot be self-optimized according to the driver's behavior. In view of the above problems, this paper proposes an LKA system based on driver's behavior habits and the road condition so that to improve the driver's confidence to use the system. Around the function, system structure, key technology and experiment verification, the following work was carried out: First, launched the driving tests to collect the driver's real lateral driving behavior. The differences of the driving parameters when driver has different driving intentions, i.e. lane keeping or not, are funded. These provide a design basis to the control decision layer. Then, proposed a joint-warning algorithm for TLC and FOD. On this basis, an adaptive adjustment method with two databases of driver profiles and lane keeping scenes are constructed. In the next step, the paper optimized the decision-making layer of LKAS. It includes 3 parts: Activation condition judgement, Driver operating status judgement and whether the system should intervene. At last, an active control algorithm based on EPS control was proposed and verified the algorithm by Simulink / Carsim.
Specific Eccentric–Isokinetic Cluster Training Improves Static Strength Elements on Rings for Elite Gymnasts

In gymnastics, coaches are constantly searching for efficient training methods in order to improve the athletes’ performance. Therefore, in this study we aimed to investigate the effects of a novel, four-week, gymnastic-specific, eccentric–isokinetic (0.1 m/s) cluster training on a computer-controlled training device on the improvement of two static strength elements on rings (swallow and support scale). Nine elite male gymnasts participated in this study. Outcome parameters were maximum strength and strength endurance in maintaining the static position of both elements. After four weeks of training, specific maximum strength increased significantly (swallow: +4.1%; d = 0.85; p = 0.01; support scale: +3.6%; d = 2.47; p = 0.0002) and strength endurance tended to improve (swallow: +104.8%; d = 0.60; p = 0.07; support scale: +26.8%; d = 0.27; p = 0.19). Our results demonstrate that top athletes can considerably improve ring-specific strength and strength endurance in only four weeks. We assumed that the high specificity but also the unfamiliar stimulus of slow eccentric movements with very long times under maximal muscle tension led to these improvements. We suggest to use this type of training periodically and during phases in which the technical training load is low.
Interchangeability between pneumococcal conjugate vaccines for pediatric use: a systematic literature review

ABSTRACT Introduction: Evidence on the interchangeability between the two pediatric pneumococcal conjugate vaccines (PCVs) – pneumococcal non-typeable Haemophilus influenzae protein D-conjugate vaccine (PHiD-CV) and 13-valent PCV (PCV13) – is limited but growing. We performed a systematic literature review to summarize evidence for PHiD-CV/PCV13 interchangeability regarding immunogenicity, safety, and effectiveness against pneumococcal disease. Areas covered: Seven records disclosing results from six studies on PHiD-CV/PCV13 interchangeability were identified. Four clinical trials showed that mixed schedules with a PHiD-CV-to-PCV13 switch at boosting or a PCV13-to-PHiD-CV switch during priming or at boosting were immunogenic with no apparent safety concerns. Two observational studies in the context of a programmatic PHiD-CV-to-PCV13 switch showed similarly high effectiveness against overall invasive pneumococcal disease with a mixed PHiD-CV/PCV13 schedule and a PCV13-only schedule. No effectiveness data for a PCV13-to-PHiD-CV switch and no immunogenicity/safety/effectiveness data for a PHiD-CV-to-PCV13 switch during priming were found. Expert opinion: For epidemiological or programmatic reasons, several local/national authorities have switched PCVs in their immunization programs. Consequently, children have received mixed schedules. Although herd immunity may obscure the individual effect, the limited data are reassuring. Additional evidence from these settings – especially effectiveness or impact data – may provide the necessary information for authorities to make informed decisions on interchanging PCVs. Video Abstract Watch the video on Vimeo. © GlaxoSmithKline Biologicals S.A. Published by Informa UK Limited, trading as Taylor & Francis Group.
Nature-Inspired Compressed Sensing for Transcriptomic Profiling From Random Composite Measurements

Transcriptomic profiling is a high-throughput approach to measure gene expression levels under different experimental conditions at different timings. With the development of the related technologies such as single-cell RNA-Seq, the dimensions of gene expression data are increased to hundreds of thousands or more for high-resolution insights. There is a long-lasting challenge in exploiting the relations between transcriptomic profiles and random composite measurements. To address it, we proposed a mathematical framework based on differential evolution (global search) with the help of compressed sensing (local search) termed as DECS. Exploiting the inherent sparse nature of gene expression data, the proposed DECS method can learn the sparse module dictionaries and levels from the low-dimensional random composite measurements for reconstructing the high-dimensional gene expression data with significant orders of magnitude (e.g. 200 $\times$ ). Several experiments were conducted to compare DECS with three benchmark methods, demonstrating that the proposed DECS outperforms the benchmark methods and can recover most of the gene expression patterns. The underlying reasons are discussed and illustrated by revealing the related mechanistic insights through extensive benchmarks on nine GSE datasets and their sensitivity analysis.
Loading and Sustained Release of Benzyl Ammonium Chloride (BAC) in Nano-Clays

Benzyl ammonium chloride (BAC) is a broad-spectrum bactericide, but vulnerable to leaching by water. In this paper, halloysite nanotubes (HNT) and montmorillonite (MMT) were used as drug carriers to load BAC, in order to achieve good anti-mildew activity and long-term sustained release properties. The HNT and MMT nano-composites were characterized by transmission electron microscope (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and nitrogen adsorption/desorption. XRD results showed that BAC intercalated the interlayer of MMT, and expanded the interlayer spacing from 1.15 nm to 1.75 nm. Pore analysis showed that BAC decreased the cavity of halloysite nanotubes to a certain extent, which indicated that BAC loaded inside the lumen of HNT successfully. TG analysis showed that the loading capacity of MMT to BAC was higher than HNT. The accelerated-release experiments revealed both two clays have significant sustained-release effects on BAC, and the releasing rate of HNT was relatively lower. Both HNT and MMT have promising application prospects as sustained-release carriers. The inhibition test showed that BAC in nano-clay has good anti-mildew resistance performance.
The effects of prolonged single night session of videogaming on sleep and declarative memory

Use of electronic media is widespread among adolescents. Many male adolescents spend a major part of their evenings playing video games. The increased exposure to artificial light as well as the exciting nature of this pastime is under suspicion to impair sleep. Sleep is considered to be important for memory consolidation, so there is also a potential risk for memory impairment due to video gaming. As learning and gaining knowledge is a very important part of adolescence, we decided to study the effects of prolonged video gaming on sleep and memory. The study was structured in a repeated measures design. Eighteen male participants played either the violent video game “Counter Strike: Global Offensive” or the board game “Monopoly” for five hours each on two Saturday nights. The game evenings were followed by sleep studies. Memory testing and vigilance evaluation was performed the next morning. During the course of the study, saliva samples were taken to determine melatonin and cortisol levels. The results of this crossover study showed slightly reduced sleep efficiency after “Counter Strike: Global Offensive” (-3.5%, p = .017) and impaired declarative memory recall (p = .005) compared to “Monopoly”. Melatonin levels at bedtime were lower after “Counter Strike: Global Offensive” (p = .005), cortisol levels were elevated while playing the video game (p = .031). Negative effects on sleep were not strong but consistent with more wake after sleep onset (+12 min) and a higher arousal index after “Counter Strike: Global Offensive”. We conclude that excessive video gaming in the evening can contribute to worsened sleep and impaired memory in male adolescents.
Engineering a Bi-Conical Microchip as Vascular Stenosis Model

Vascular stenosis is always associated with hemodynamic changes, especially shear stress alterations. Herein, bi-conical shaped microvessels were developed through flexibly and precisely controlled templated methods for hydrogel blood-vessel-like microchip. The blood-vessel-like microvessels demonstrated tunable dimensions, perfusable ability, and good cytocompatibility. The microchips showed blood-vessel-like lumens through fine embeddedness of human umbilical vein endothelial cells (HUVECs) on the interior surface of hydrogel microchannels, which closely reproduced the morphology and functions of human blood vessels. In the gradual narrowing region of bi-conical shape, fluid flow generated wall shear stress, which caused cell morphology variations. Wall shear rates at the gradual narrowing region were simulated by FLUENT software. The results showed that our microchannels qualified for performance as a vascular stenosis-like model in evaluating blood hydrodynamics. In general, our blood-vessel-on-a-chip could offer potential applications in the prevention, diagnosis, and therapy of arterial thrombosis.
Changing of the guard: How the Lyme disease spirochete subverts the host immune response

Lyme disease, also known as Lyme borreliosis, is the most common tick-transmitted disease in the Northern Hemisphere. The disease is caused by the bacterial spirochete Borrelia burgdorferi and other related Borrelia species. One of the many fascinating features of this unique pathogen is an elaborate system for antigenic variation, whereby the sequence of the surface-bound lipoprotein VlsE is continually modified through segmental gene conversion events. This perpetual changing of the guard allows the pathogen to remain one step ahead of the acquired immune response, enabling persistent infection. Accordingly, the vls locus is the most evolutionarily diverse genetic element in Lyme disease–causing borreliae. Small stretches of information are transferred from a series of silent cassettes in the vls locus to generate an expressed mosaic vlsE gene version that contains genetic information from several different silent cassettes, resulting in ∼1040 possible vlsE sequences. Yet, despite its extreme evolutionary flexibility, the locus has rigidly conserved structural features. These include a telomeric location of the vlsE gene, an inverse orientation of vlsE and the silent cassettes, the presence of nearly perfect inverted repeats of ∼100 bp near the 5′ end of vlsE, and an exceedingly high concentration of G runs in vlsE and the silent cassettes. We discuss the possible roles of these evolutionarily conserved features, highlight recent findings from several studies that have used next-generation DNA sequencing to unravel the switching process, and review advances in the development of a mini-vls system for genetic manipulation of the locus.
Disrupted brain functional hub and causal connectivity in acute mild traumatic brain injury

There have been an increasing number of functional magnetic resonance imaging (fMRI) reports on brain abnormalities in mild traumatic brain injury (mTBI) at different phases. However, the neural bases and cognitive impairment after acute mTBI are unclear. This study aimed to identify brain functional hubs and connectivity abnormalities in acute mTBI patients and their correlations with deficits in cognitive performance. Within seven days after brain injury, mTBI patients (n=55) and age-, sex-, and educational -matched healthy controls (HCs) (n=41) underwent resting-state fMRI scans and cognitive assessments. We derived functional connectivity (FC) strength of the whole-brain network using degree centrality (DC) and performed Granger causality analysis (GCA) to analyze causal connectivity patterns in acute mTBI. Compared with HCs, acute mTBI patients had significantly decreased network centrality in the left middle frontal gyrus (MFG). Additionally, acute mTBI showed decreased inflows from the left MFG to bilateral middle temporal gyrus (MTG), left medial superior frontal gyrus (mSFG), and left anterior cingulate cortex (ACC). Correlation analyses revealed that changes in network centrality and causal connectivity were associated with deficits in cognitive performance in mTBI. Our findings may help to provide a new perspective for understanding the neuropathophysiological mechanism of acute cognitive impairment after mTBI.
Use of the wearable smart glasses for indocyanine green (ICG) angiography of a flap surgery

Dear Editor, Wearable technology with heads-up displays has entered the medical field and been used for various medical purposes such as navigation surgery (Shao et al., 2014), education (Guze, 2015), and vital sign monitoring (Liebert, Zayed, Aalami, Tran, & Lau, 2016). In the setting of the reconstructive surgery, near-infrared fluorescence (NIRF) imaging using indocyanine green (ICG), also known as ICG angiography, is used predominantly to assess tissue perfusion in transferred flap (Pruimboom et al., 2019). Our goal in this letter is to describe a new effective method for intraoperative ICG angiography for flap surgery using wearable smart glasses. PicoLinker (Westunitis Co., Ltd., Osaka, Japan) is a kind of wearable glasses with a lightweight monocular head-mounted display that can display images or videos that are on existing monitor screens. It contains a prism monitor with resolution of 640 × 360 pixels and can be attached to the normal glasses easily. We hypothesized that PicoLinker can be used as an alternative screen of NIRF imaging for evaluating flap vascularity. A 42-year-old woman underwent left mastectomy and immediate reconstruction with a deep inferior epigastric artery perforator (DIEP) flap was planned. NIRF image monitor was connected to the PicoLinker to be projected on the prism monitor. After the DIEP flap was elevated, ICG angiography was performed using a Lightvision (Shimadzu Co., Kyoto, Japan). After an intravenous bolus injection of 1 ml ICG, an evaluation of ICG angiography was performed. The surgeon marked the border of the nonenhanced area and the enhanced area according to the image on the prism monitor of the PicoLinker (Figure 1A,B). This method using a PicoLinker for ICG angiography of the flap has several advantages. First, using this method, the surgeon can glance at the fluorescent image of the ICG angiography on the PicoLinker while keeping one's eye on the operation field. This would improve the accuracy of the marked line of the enhanced area in the flap. Second, this device is small and light (30 g). Using this device, a large monitor previously used for ICG angiography is not needed. Therefore, we can vacate the space in the operation room. While further investigations will be required, this method using a PicoLinker for ICG angiography of the flap has the potential to be a useful evaluating tool.