Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and molecular-based identification of bacteria from unhatched leftover eggs of ducks in selected mini-hatcheries of Kishoreganj, Bangladesh

Objectives: The study was designed for isolation and identification of the bacteria present in unhatched leftover eggs of duck in selected mini-hatcheries of Kishoreganj, Bangladesh. Materials and Methods: A total of 54 unhatched discarded eggs were collected as samples from different mini-hatcheries of Tarail and Itna Upazilas of Kishoreganj and aseptically carried to the laboratory in the icebox. Surface washings (n = 54) and inner contents (n = 54) were collected and enriched in Luria–Bertani broth followed by the isolation of pure colonies of different bacteria onto eosin methylene blue agar, mannitol salt agar, Salmonella–Shigella agar, and blood agar plates. Identification of the bacterial isolates was done by cultural properties, staining, and biochemical tests followed by molecular detection by Polymerase chain reaction. Results: Of 108 samples, 62 were found positive for Salmonella spp. (76%), 59 for E. coli (54%), 52 for Staphylococcus spp. (48%), and 5 for Clostridium spp. (9%). From the egg surface samples, Staphylococcus spp. were recovered in the highest (67%) followed by Salmonella spp. (59%), E. coli (56%), and Clostridium spp. (9%). From the inner contents of eggs, Salmonella spp. were recovered in the highest (56%), followed by E. coli (53%) and Staphylococcus spp. (30%). Conclusion: The isolated bacteria might be associated with the decreased hatchability and embryo mortality in the mini-hatcheries of duck.
Discovery of the oldest known biomarkers provides evidence for phototrophic bacteria in the 1.73 Ga Wollogorang Formation, Australia

The discovery of mid‐Proterozoic (1.8–0.8 billion years ago, Ga) indigenous biomarkers is a challenge, since biologically informative molecules of such antiquity are commonly destroyed by metamorphism or overprinted by drilling fluids and other anthropogenic petroleum products. Previously, the oldest clearly indigenous biomarkers were reported from the 1.64 Ga Barney Creek Formation in the northern Australian McArthur Basin. In this study, we present the discovery of biomarker molecules from carbonaceous shales of the 1.73 Ga Wollogorang Formation in the southern McArthur Basin, extending the biomarker record back in time by ~90 million years. The extracted hydrocarbons illustrate typical mid‐Proterozoic signatures with a large unresolved complex mixture, high methyl alkane/n‐alkane ratios and the absence of eukaryotic steranes. Acyclic isoprenoids, saturated carotenoid derivatives, bacterial hopanes and aromatic hopanoids and steroids also were below detection limits. However, continuous homologous series of low molecular weight C14–C19 2,3,4‐ and 2,3,6‐trimethyl aryl isoprenoids (AI) were identified, and C20–C22 AI homologues were tentatively identified. Based on elevated abundances relative to abiogenic isomers, we interpret the 2,3,6‐AI isomer series as biogenic molecules and the 2,3,4‐AI series as possibly biogenic. The biological sources for the 2,3,6‐AI series include carotenoids of cyanobacteria and/or green sulphur bacteria (Chlorobiaceae). The lower concentrated 2,3,4‐AI series may be derived from purple sulphur bacteria (Chromatiaceae). These degradation products of carotenoids are the oldest known clearly indigenous molecules of likely biogenic origin.
Continuation of Buprenorphine to Facilitate Postoperative Pain Management for Patients on Buprenorphine Opioid Agonist Therapy.

BACKGROUND Acute pain management in patients on buprenorphine opioid agonist therapy (BOAT) can be challenging. It is unclear whether BOAT should be continued or interrupted for optimization of postoperative pain control. OBJECTIVES To determine an evidence-based approach for pain management in patients on BOAT in the perioperative setting, particularly whether BOAT should be continued or interrupted with or without bridging to another mu opioid agonist and to identify benefits and harms of either perioperative strategy. STUDY DESIGN Systematic literature review with qualitative data synthesis. SETTING Hospital, perioperative. METHODS The study protocol was registered on PROSPERO (Registration number 9030276355). Medline via OVID, EMBASE, CINAHL, and the Cochrane CENTRAL register of trials were searched for prospective or retrospective observational or controlled studies, case series, and case reports that described perioperative or acute pain care for patients on BOAT. References of narrative and systematic reviews addressing acute pain management in patients on BOAT and references of included articles were hand-searched to identify additional original articles for inclusion. The full text of publications were reviewed for final inclusion, and data were extracted using a standardized data extraction form. Results were summarized qualitatively. Primary outcomes were postoperative pain intensity and total opioid use and identification of benefits and harms of perioperative strategies. RESULTS Eighteen publications presenting data on the perioperative management of patients on BOAT were identified: 10 case reports, 5 case series, and 3 retrospective cohort studies. Eleven articles reported continuation of BOAT, 2 concerned bridging BOAT, and 4 articles described stopping BOAT without planned bridging. In one retrospective cohort study, BOAT was continued in half and interrupted in half of patients. Patients on BOAT may have pain that is more difficult to treat than those who are not on OAT. There is no clear evidence that one particular strategy provides superior postoperative pain control, but interruption of BOAT may result in harm, including failure to return to baseline BOAT doses, continuing non-BOAT opioid use, or relapse of opioid use disorder. LIMITATIONS There were a limited number of articles relevant to the study question consisting of case reports and retrospective observational studies. Some omitted relevant details. No prospective studies were found. CONCLUSIONS There is no clear benefit to bridging or stopping BOAT but failure to restart it may pose concerns for relapse. We recommend continuing BOAT in the perioperative period when possible and incorporating an interdisciplinary approach with multimodal analgesia. KEY WORDS Opioid use disorder, opiate substitution treatment, buprenorphine, buprenorphine-naloxone, buprenorphine opioid agonist therapy, postoperative pain, acute pain, multimodal analgesia.
In Vitro Bioactivity and Biocompatibility of Bio-Inspired Ti-6Al-4V Alloy Surfaces Modified by Combined Laser Micro/Nano Structuring

The bioactivity and biocompatibility play key roles in the success of dental and orthopaedic implants. Although most commercial implant systems use various surface microstructures, the ideal multi-scale topographies capable of controlling osteointegration have not yielded conclusive results. Inspired by both the isotropic adhesion of the skin structures in tree frog toe pads and the anisotropic adhesion of the corrugated ridges on the scales of Morpho butterfly wings, composite micro/nano-structures, including the array of micro-hexagons and oriented nano-ripples on titanium alloy implants, were respectively fabricated by microsecond laser direct writing and femtosecond laser-induced periodic surface structures, to improve cell adherence, alignment and proliferation on implants. The main differences in both the bioactivity in simulated body fluid and the biocompatibility in osteoblastic cell MC3T3 proliferation were measured and analyzed among Ti-6Al-4V samples with smooth surface, micro-hexagons and composite micro/nano-structures, respectively. Of note, bioinspired micro/nano-structures displayed the best bioactivity and biocompatibility after in vitro experiments, and meanwhile, the nano-ripples were able to induce cellular alignment within the micro-hexagons. The reasons for these differences were found in the topographical cues. An innovative functionalization strategy of controlling the osteointegration on titanium alloy implants is proposed using the composite micro/nano-structures, which is meaningful in various regenerative medicine applications and implant fields.
Genome Sequence of Komagataeibacter saccharivorans Strain JH1, Isolated from Fruit Flies

We present the genome sequence of Komagataeibacter saccharivorans strain JH1, which belongs to the acetic acid bacteria. The draft genome sequence consists of 3.7 Mb and contains 3,437 predicted protein-encoding genes. This organism contains putative genes involved in cellulose and levan biosynthesis. ABSTRACT We present the genome sequence of Komagataeibacter saccharivorans strain JH1, which belongs to the acetic acid bacteria. The draft genome sequence consists of 3.7 Mb and contains 3,437 predicted protein-encoding genes. This organism contains putative genes involved in cellulose and levan biosynthesis.
Pharmacokinetic-Pharmacodynamic-Efficacy Modeling of ONO-7579, a Novel Pan–Tropomyosin Receptor Kinase Inhibitor, in a Murine Xenograft Tumor Model

The orally available and novel small molecule ONO-7579 (N-{2-[4-(2-amino-5-chloropyridin-3-yl)phenoxy]pyrimidin-5-yl}-N′-[2-(methanesulfonyl)-5-(trifluoromethyl)phenyl]urea) is a highly potent and selective pan–tropomyosin receptor kinase (TRK) inhibitor. The objective of the present study was to characterize the pharmacokinetic (PK), pharmacodynamic (PD), and antitumor efficacy relationships of ONO-7579 in mice xenografted with a human colorectal cancer cell line, KM12 (harboring the tropomyosin 3 (TPM3)-neurotrophic tyrosine receptor kinase 1 fusion gene), via a PK/PD modeling approach. Plasma and tumor concentrations of ONO-7579, tumor levels of phosphorylated TPM3-TRKA (pTRKA), and tumor volumes in the murine model were measured with a single or multiple dose of ONO-7579 (0.06–0.60 mg/kg) administered once daily. The PK/PD/efficacy models were developed in a sequential manner. Changes in plasma concentrations of ONO-7579 were described with an oral one-compartment model. Tumor concentrations of ONO-7579 were higher than plasma concentrations, and changes in ONO-7579 tumor concentrations were described with an additional tumor compartment that had no influence on plasma concentrations. pTRKA in tumors was described with a direct Emax model, and the tumor ONO-7579 concentration causing 50% of the maximum effect was estimated to be 17.6 ng/g. In addition, a pTRKA-driven tumor growth inhibition model indicated that ONO-7579 started to sharply increase the antitumor effect at pTRKA inhibition rates >60% and required >91.5% to reduce tumors. In conclusion, the developed PK/PD/efficacy models revealed a “switch-like” relationship between pTRKA inhibition rate and antitumor effect in a murine KM12 xenograft model, demonstrating that pTRKA in tumors could serve as an effective biomarker for scheduling the dose regimen in early-stage clinical studies. SIGNIFICANCE STATEMENT In recent years, clinical development of TRK inhibitors in patients with neurotrophic tyrosine receptor kinase fusion–positive solid tumors has been accelerated. This research found that phosphorylated TRKA was a useful biomarker for explaining the antitumor efficacy of TRK inhibitors using a pharmacokinetic/pharmacodynamic modeling approach in xenograft mice. This finding suggests a rational dosing regimen in early-stage clinical studies for ONO-7579 (N-{2-[4-(2-amino-5-chloropyridin-3-yl)phenoxy]pyrimidin-5-yl}-N′-[2-(methanesulfonyl)-5-(trifluoromethyl)phenyl]urea), a novel pan-TRK inhibitor.
Sleep Disordered Breathing in Hypertrophic Cardiomyopathy—Current State and Future Directions

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiomyopathy and sleep disordered breathing (SDB) is a treatable risk factor that has been seen to occur concurrently, and is known to propagate mortality and morbidity in a number of cardiovascular disease states including heart failure, and indeed hypertrophic cardiomyopathy. In this review, we summarize past studies that explored the simultaneous occurrence of HCM and SDB, and the pathophysiology of SDB in relation to heart failure, arrhythmias, cardiac ischemia and pulmonary hypertension in HCM. The current therapeutic modalities, with the effect of obstructive sleep apnea (OSA) treatment on HCM, are then discussed along with potential future directions.
Naive Gabor Networks for Hyperspectral Image Classification

Recently, many convolutional neural network (CNN) methods have been designed for hyperspectral image (HSI) classification since CNNs are able to produce good representations of data, which greatly benefits from a huge number of parameters. However, solving such a high-dimensional optimization problem often requires a large number of training samples in order to avoid overfitting. In addition, it is a typical nonconvex problem affected by many local minima and flat regions. To address these problems, in this article, we introduce the naive Gabor networks or Gabor-Nets that, for the first time in the literature, design and learn CNN kernels strictly in the form of Gabor filters, aiming to reduce the number of involved parameters and constrain the solution space and, hence, improve the performances of CNNs. Specifically, we develop an innovative phase-induced Gabor kernel, which is trickily designed to perform the Gabor feature learning via a linear combination of local low-frequency and high-frequency components of data controlled by the kernel phase. With the phase-induced Gabor kernel, the proposed Gabor-Nets gains the ability to automatically adapt to the local harmonic characteristics of the HSI data and, thus, yields more representative harmonic features. Also, this kernel can fulfill the traditional complex-valued Gabor filtering in a real-valued manner, hence making Gabor-Nets easily perform in a usual CNN thread. We evaluated our newly developed Gabor-Nets on three well-known HSIs, suggesting that our proposed Gabor-Nets can significantly improve the performance of CNNs, particularly with a small training set.
Engagement with a Web-Based Health Promotion Intervention among Vocational School Students: A Secondary User and Usage Analysis

Engagement with web-based interventions is both generally low and typically declining. Visits and revisits remain a challenge. Based on log data of a web-based cluster randomized controlled trial conducted in vocational schools, the present secondary analysis aimed to identify influencing factors on initially logging in to a health promotion platform among young adults and to examine the engagement over the course of an eight-week intervention. Data of 336 students (62.2% female, age span 18–25) from two intervention arms (web-based intervention and web-based intervention with an additional initial face-to-face contact) was included. Binary logistic regression and log-data visualization were performed. An additional initial face-to-face contact (odds ratio (OR) = 2.971, p = 0.005), female sex (OR = 2.237, p = 0.046) and the health-related skill “dealing with health information” (OR = 2.179, p = 0.030) significantly increased the likelihood of initially logging in. Other variables showed no influence. 16.6% of all potential users logged in at least once, of which 57.4% revisited the platform. Most logins were tracked at the beginning of the intervention and repeated engagement was low. To increase the engagement with web-based interventions, health-related skills should be fostered. In addition, a strategy could be to interlink comparable interventions in vocational schools more regularly with everyday teaching through multi-component interventions.
Impact of Long-term Employment of a Self-Management Program in Asthmatics

Background: Self-management of asthmatics is thought to facilitate early detection and treatment of asthma exacerbations, and to reduce asthma-related morbidity and mortality. Aim: To evaluate the efficacy of a self-management program on the long-term follow-up of asthma and determine the factors influencing the success of such program in asthmatic patients. Methods: Objective parameters (criteria of asthma control, FEV1 and FEV1/FVC) were assessed at inclusion and at the end of the retrospective study, 8.9±8 years later, using a 1-year recall patient-based questionnaire and lung function measurements. Results: Among the 112 patients who answered the questionnaire (63% of response), 69 patients followed the self-management program, either partially with the help of a phone call to their physician (22%) or exclusively (78%), the latter displaying higher education levels (p<0.05). In the “self-management” group, GINA status was stabilized or improved (80%), FEV1 was significantly improved, a less frequent use of emergency services was reported, corticosteroid dependence was reduced (22% vs. 7%, p=0.03) and smoking dropped (p=0.05). Additionally, higher global quality of life scores were obtained in the self-management group (21% vs. 7.9%, p= 0.05). Conclusion: A self-management program significantly improved control of asthma and quality of life of asthmatics. Because control of asthma is lacking for the vast majority of asthmatics, these results argue for an usual employment of such program in the long term follow-up of asthmatics.
High-density electrophysiological recordings in macaque using a chronically implanted 128-channel passive silicon probe

Objective. The analysis of interactions among local populations of neurons in the cerebral cortex (e.g. within cortical microcolumns) requires high resolution and high channel count recordings from chronically implanted laminar microelectrode arrays. The request for high-density recordings of a large number of recording sites can presently only be accomplished by probes realized using complementary metal-oxide-semiconductor (CMOS) technology. In preparation for their use in non-human primates, we aimed for neural probe validation in a head-fixed approach analyzing the long-term recording capability. Approach. We examined chronically implanted silicon-based laminar probes, realized using a CMOS technology in combination with micromachining, to record from the primary visual cortex (V1) of a monkey. We used a passive CMOS probe that had 128 electrodes arranged at a pitch of 22.5 µm in four columns and 32 rows on a slender shank. In order to validate the performance of a dedicated microdrive, the overall dimensions of probe and interface boards were chosen to be compatible with the final active CMOS probe comprising integrated circuitry. Main results. Using the passive probe, we recorded simultaneously local field potentials (LFP) and spiking multiunit activity (MUA) in V1 of an awake behaving macaque monkey. We found that an insertion through the dura and subsequent readjustments of the chronically implanted neural probe was possible and allowed us to record stable LFPs for more than five months. The quality of MUA degraded within the first month but remained sufficiently high to permit mapping of receptive fields during the full recording period. Significance. We conclude that the passive silicon probe enables semi-chronic recordings of high quality of LFP and MUA for a time span exceeding five months. The new microdrive compatible with a commercial recording chamber successfully demonstrated the readjustment of the probe position while the implemented plug structure effectively reduced brain tissue movement relative to the probe.
Detecting Sleep Using Heart Rate and Motion Data from Multisensor Consumer-Grade Wearables, Relative to Wrist Actigraphy and Polysomnography.

STUDY OBJECTIVES Multisensor wearable consumer devices allowing collection of multiple data sources, such as heart rate and motion, for the evaluation of sleep in the home environment, are increasingly ubiquitous. However, the validity of such devices for sleep assessment has not been directly compared to alternatives such as wrist actigraphy or PSG. METHODS Eight participants each completed four nights in a sleep laboratory, equipped with polysomnography (PSG) and several wearable devices. RPSGT-scored PSG served as ground truth for sleep-wake state. Wearable devices providing sleep-wake classification data were compared to PSG at both an epoch-by-epoch and night level. Data from multisensor wearables (Apple Watch and Oura Ring) were compared to data available from ECG and a tri-axial wrist actigraph to evaluate quality and utility of heart rate and motion data. Machine learning methods were used to train and test sleep-wake classifiers, using data from consumer wearables. Quality of classifications derived from devices were compared. RESULTS For epoch-by-epoch sleep-wake performance, research devices ranged in d' between 1.771 and 1.874, with sensitivity between 0.912 and 0.982, and specificity between 0.366 and 0.647. Data from multisensor wearables were strongly correlated at an epoch-by-epoch level with reference data sources. Classifiers developed from the multisensor wearable data ranged in d' between 1.827 and 2.347, with sensitivity between 0.883 and 0.977, and specificity between 0.407 and 0.821. CONCLUSIONS Data from multisensor consumer wearables is strongly correlated with reference devices at the epoch level and can be used to develop epoch-by-epoch models of sleep-wake rivaling existing research devices.
High‐throughput screening of argan oil composition and authenticity using benchtop 1H NMR

Abstract We use 60‐MHz benchtop nuclear magnetic resonance (NMR) to acquire 1H spectra from argan oils of assured origin. We show that the low‐field NMR spectrum of neat oil contains sufficient information to make estimates of compositional parameters and to inform on the presence of minor compounds. A screening method for quality and authenticity is presented based on nearest‐neighbour outlier detection. A variety of oil types are used to challenge the method. In a survey of retail‐purchased oils, several instances of fraud were found.
Effects of inoculants on the fermentation characteristics and in vitro digestibility of reed canary grass (Phalaris arundinacea L.) silage on the Qinghai-Tibetan Plateau.

To effectively use local available grass resources to cover the winter feed shortage on the Qinghai-Tibetan Plateau, direct-cut and wilted reed canary grass (RCG) silages were prepared by using a rolled-bale system, and their ensiling characteristics and in vitro digestibility were studied. Silages were treated without (control) or with inoculants including LP (Lactobacillus plantarum), LPLB (L. plantarum, L. buchneri), and LPLBc (L. plantarum, L. buchneri, and cellulase), and were stored at ambient temperature (5.7-14.6°C) for 90 days. Compared with control, the inoculated silages increased (p < .05) lactic acid and acetic acid contents, and reduced (p < .05) final pH value and ammonia-N ratio of total N. The highest WSC content (41.2 g/kg DM) occurred for LPLB-inoculated silage, whereas LPLBc-treated silage displayed the lowest contents of NDF (522.9 g/kg DM) and ADF (275.5 g/kg DM). In addition, LPLBc-inoculated silage had the highest in vitro gas production (51.0 ml/g DM), in vitro DM digestibility (619.3 g/kg DM), and metabolic energy (9.6 kJ/kg DM). These results confirmed that treatments with inoculants at ensiling could improve silage fermentation and in vitro digestibility of RCG, and this could be a potential winter feed for animals on the Qinghai-Tibetan Plateau.