Miracle-dz/UniFAR-FTUs huggingface dataset:
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Abstract Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees. The speed and accuracy of GraftM was benchmarked with in silico and in vitro mock communities using taxonomic markers, and was found to have higher accuracy at the family level with a processing time 2.0–3.7× faster than currently available software. Exploration of a wetland metagenome using 16S rRNA- and methyl-coenzyme M reductase (McrA)-specific gpkgs revealed taxonomic and functional shifts across a depth gradient. Analysis of the NCBI nr database using the McrA gpkg allowed the detection of novel sequences belonging to phylum-level lineages. A growing collection of gpkgs is available online (https://github.com/geronimp/graftM_gpkgs), where curated packages can be uploaded and exchanged.
Thematic segmentation of meetings through document/speech alignment

This article proposes a multimodal approach for segmenting meeting recordings. This bi-modal method takes advantages of the alignment of speech transcript with documents, in the context of meetings or lectures, where documents are discussed. The method first displays the alignment results as a set of nodes in a 2D space, where the two axes represent respectively the documents content and the speech transcript. The most connected regions in this graph are detected using a clustering method. The final clusters are then projected on the speech axis. Finally, the obtained sequence of segments is considered as the thematic structure of the speech transcript. In this article, we present our bi-modal method and compare it with two other mono-modal thematic segmentation methods.
Detecting Memory Impairment in Deaf People: A New Test of Verbal Learning and Memory in British Sign Language.

OBJECTIVE Most existing tests of memory and verbal learning in adults were created for spoken languages, and are unsuitable for assessing deaf people who rely on signed languages. In response to this need for sign language measures, the British Sign Language Verbal Learning and Memory Test (BSL-VLMT) was developed. It follows the format of the English language Hopkins Verbal Learning Test Revised, using standardized video-presentation with novel stimuli and instructions wholly in British Sign Language, and no English language requirement. METHOD Data were collected from 223 cognitively healthy deaf signers aged 50-89 and 12 deaf patients diagnosed with dementia. Normative data percentiles were derived for clinical use, and receiver-operating characteristic curves computed to explore the clinical potential and diagnostic sensitivity and specificity. RESULTS The test showed good discrimination between the normative and clinical samples, providing preliminary evidence of clinical utility for identifying learning and memory impairment in older deaf signers with neurodegeneration. CONCLUSIONS This innovative video testing approach transforms the ability to accurately detect memory impairments in deaf people and avoids the problems of using interpreters, with international potential for adapting similar tests into other signed languages.
Image Watermarking Using 3-Level Discrete Wavelet Transform (DWT)

We have implemented a robust image watermarking technique for the copyright protection based on 3-level discrete wavelet transform (DWT). In this technique a multi-bit watermark is embedded into the low frequency sub-band of a cover image by using alpha blending technique. The insertion and extraction of the watermark in the grayscale cover image is found to be simpler than other transform techniques. The proposed method is compared with the 1-level and 2-level DWT based image watermarking methods by using statistical parameters such as peak-signal-to-noise-ratio (PSNR) and mean square error (MSE). The experimental results demonstrate that the watermarks generated with the proposed algorithm are invisible and the quality of watermarked image and the recovered image are improved.
A New Negative Output Buck–Boost Converter with Wide Conversion Ratio

In this paper, a new negative output (N/O) buck–boost converter, which can be applied for applications that need wide range of inverse voltage, is proposed. The steady-state, small-signal model and power losses of the proposed converter operating in a continuous conduction mode are analyzed. Comparisons among the traditional buck–boost converter, N/O hybrid buck–boost converter and N/O self-lift Luo converter are presented, and it is found that the proposed converter possesses a widest voltage conversion ratio in these four converters. Finally, a prototype is built, and the simulated waveforms from the PSIM software and the experimental results are presented for validation.
Assessment of Ovine Johne’s disease in the Mandya sheep breed in South India using multiple diagnostic tests and bio-typing of Mycobacterium avium subspecies paratuberculosis infection

Abstract Johne’s disease is major infectious disease of domestic livestock in India. Despite low per animal productivity, the country is yet to initiate plan for the survey and control of disease at National scale. A total of 81 clinical samples from Mandya breed of sheep were collected from an organised farm (Livestock Research and Information Centre, Nagmangala) and farmer’s flocks suspected for Johne’s disease on the basis of clinical symptoms (weakness, emaciation, diarrhea and alopecia). Only 10.0% samples from two farms were screened for bio-load of Mycobacterium avium subspecies paratuberculosis (MAP) using multiple tests (microscopy, indigenous ELISA, IS900 PCR and culture). Results showed that 100.0% samples were positive for MAP infection both in microscopy and “Indigenous ELISA”. IS1311 PCR-REA bio-typed 60.0% (feces) and 100.0% (blood and tissue) isolates as “Indian Bison Type”. Typing investigated for the first time that biotype was of Indian origin and present in sheep flocks of South India having wide geographical distribution and broad host range. Study reported high bio-load of MAP in Mandya breed of sheep in Nagamangala, Mandya district and Bilagi taluk of Bagalkot district in South India. Being Johne’s disease a spectral disease, multiple tests were useful for the screening of MAP infection in sheep farms. Study emphasised the need for initiation of short and long term control programs to reduce production losses and sharing of MAP strains by other domestic livestock species and prevent contamination of human food chain and reduce risk to human population.
An Efficient Gyro-Aided Optical Flow Estimation in Fast Rotations With Auto-Calibration

Optical flow (OF) measures the displacement of the projections of visual landmarks on the image plane and is widely used for motion and structure estimations. Fast rotational motion results in large image motion and poses a major challenge to many OF algorithms. To improve the performance of OF estimations, gyroscopes can be adopted to predict the image motion between adjacent frames when the camera motion is dominated by rotation. This paper first proposes an offline method for calibrating the camera focal length, gyroscope bias, the relative orientation and time offset between the camera and gyroscopes without using a man-made target. Then a simple and efficient method is proposed to aid the OF computation with the gyroscope readings. Our approach is evaluated using a low-cost endoscope-gyroscope system and shows improved visual tracking performance as compared to the stand-alone OF algorithm. The method is suited for use on lightweight platforms equipped with gyroscopes and an endoscopic camera, which potentially can provide efficient image guidance in endoscopic procedures.
Glaucoma Optical Coherence Tomography Angiography Macular and Peripapillary Vessel Perfusion Density in Healthy Subjects , Glaucoma Suspects , and Glaucoma Patients

Giacinto Triolo, Alessandro Rabiolo, Nathan D. Shemonski, Ali Fard, Federico Di Matteo, Riccardo Sacconi, Paolo Bettin, Stephanie Magazzeni, Giuseppe Querques, Luis E. Vazquez, Piero Barboni, and Francesco Bandello Department of Ophthalmology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy Carl Zeiss Meditec, Inc., Dublin, California, United States Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
Microscopic Characterization of Cellulose Nanocrystals Isolated from Sisal Fibers

Isolation of cellulose nanocrystals (CNCs) was carried out by unrepeated or repeated alkalization and bleaching followed by sulfuric acid hydrolysis and air cooling (unrepeated) or ice cooling (repeated). The influence of unrepeated and repeated alkalization and bleaching, and cooling rate (cooling medium) after hydrolysis on the morphology and crystallinity of the isolated micro- and nano-celluloses were characterized. Scanning electron microscopy (SEM) showed that repeated alkalization and bleaching led to a higher degree of fibrillated microcellulose (~10 mm) with higher surface roughness than unrepeated alkalization and bleaching. Transmission electron microscopy (TEM) revealed that air and ice cooling after acid hydrolysis producing different CNCs morphologies; heterogeneous CNCs nanowhisker and nano-spherical (~50 nm), and homogenous CNCs nanowhiskers (~50 nm width and ~500 nm length), respectively. The homogeneous nano whisker was related to single phase monoclinic b-cellulose. Residual lignin agglutinating between the nanoparticles was observed in TEM image as well as in Fourier transform infrared (FTIR) spectra. The existence of residual lignin after hydrolysis is comparable in crystalinity (crystallinity index, Ic: ~91%) with that of isolated CNCs, as confirmed by x-ray diffraction (XRD) analysis.
Cytotoxicity assessment of synthesized nickel oxide nanoparticles on MCF-7 and A-549 cancer cell lines

The main focus of this study was to assess the cytotoxicity of synthesized Nickel oxide nanoparticles on some human cancer cell lines like MCF7 AND A-549. The assessment was done by using MTT assay. The Nickel oxide nanoparticles were synthesized by simple solution method. The cytotoxicity studies were made on the human cancer lines along with the normal cell lines using the synthesized Nickel oxide nanoparticles by in vitro method using MTT assay model. From the observations it was found that the synthesized Nickel oxide nanoparticles were more active towards the cancer cells with less toxicity.The NiO-Ace nanoparticles possess significant cytotoxic activity (IC50 =11.46) against the tested cell lines.
Real-Time Intraoperative Computed Tomography to Assist Cochlear Implant Placement in the Malformed Inner Ear

Objective: Cochlear implantation is increasingly being performed in children with inner ear malformations. In severe cochleovestibular anomalies, such as severe partitioning defects and common cavity dysplasia, positioning of the electrode array can be hazardous, with inadvertent placement into the internal auditory canal (IAC) or carotid canal being well known. We describe a case in which real-time intraoperative computed tomographic scanning was used to help achieve proper electrode positioning in a child with a severe malformation. Patient: Child with common cavity malformations undergoing cochlear implantation. Intervention: Intraoperative computed tomography used during implantation procedure. Main Outcome Measure Use of technique in determining electrode position. Results: A 10-year-old patient with bilateral common cavity malformations presented with declining performance in a functioning implant placed 7 years earlier. The family elected implantation of the contralateral ear. Via a posterior labyrinthotomy approach, a straight array was placed into the common cavity. Intraoperative computed tomographic scanning was immediately performed on the operating room table, showing that the array was in the IAC. A second attempt with a different insertion angle also resulted in IAC placement. In a third attempt, the electrode was advanced as a loop, grasping the tip through an adjacent second labyrinthotomy. Computed tomography confirmed good position against the outer wall of the cavity. Conclusion: Real-time intraoperative computed tomography is a new technology with many potential applications in surgery. In our patient, it allowed rapid and accurate determination of electrode position and helped achieve ideal placement in a severely malformed inner ear.
Family Coaching as a delivery modality for evidence-based prevention programs

Family Coaching is proposed as a new delivery format for evidence-based prevention programs (EBPPs). Three recent developments in health promotion support the potential efficacy of Family Coaching: (1) renewed interest in integrated prevention programs for multiple risk factors and behavior changes, (2) broad and long-term impacts of family-based interventions, and (3) popular acceptance of “coaching” as a nonstigmatizing, goal-focused intervention strategy. Family coaches are community members and paraprofessionals trained in common elements of EBPP. Family Coaching has specific goals, is short term, and has definable outcomes. Coaches frame the program’s goals to be consistent with the family’s values, normalize the family’s experience, assess their strengths, and help the family set goals and develop skills and routines to problem solve challenging situations. Broad dissemination of EBPP will be facilitated with delivery formats that are flexible to meet families’ priorities and providers’ desires and capacities to tailor programs to local contexts.
Electrochemotherapy for Non-melanoma Skin Cancer in a Child with Xeroderma Pigmentosum.

fourth ECT session. Following a biopsy from the lesion, our tumour board decided to refer the patient to a hand surgeon. Removal of the SCC was possible only with amputation of the fourth digit. None of the lesions showing CR relapsed during the follow-up period (4–15 months). Pain was not observed following the ECT sessions. We observed sore muscles, mild and transient erythema and oedema around the treated lesions. During the healing process, 2–3 weeks after ECT, central or complete necrosis developed in the treated tumours. Skin marks from the needle electrodes were visible for approximately one month. No systemic side-effects were observed, and the lung functional tests following the ECT sessions were normal. Due to her disease, our patient also had microstoma, ectropion and disfiguring scarring of the midface and upper lip. The patient had difficulty closing her eyelids and eating, with intubation also posing a challenge during general anaesthesia. Combined with ECT sessions, re-constructive surgeries were performed, and the function of the eyelids and lips improved significantly. Residual tumours were not detected with a histological examination of the lesions, which, clinically, had a CR.
Emergence of cancer stem cells in head and neck squamous cell carcinoma: A therapeutic insight with literature review

Accumulating evidence suggests that self-renewal and differentiation capabilities reside only in a subpopulation of tumor cells, termed cancer stem cells (CSCs), whereas the remaining tumor cell population lacks the ability to initiate tumor development or support continued tumor growth. In head and neck squamous cell carcinoma (HNSCC), as with other malignancies, CSCs have been increasingly shown to have an integral role in tumor initiation, disease progression, metastasis, and treatment resistance. In this article, the author summarizes the current knowledge of the role of CSCs in HNSCC and discusses the therapeutic implications and future directions of this field.
Ventricular ectopic beats classification using Sparse Representation and Gini Index

In this study, we consider using sparse representation and the Gini Index (GI) for Arrhythmia classification. Our approach involves, first, designing a separate dictionary for each Arrhythmia class using a set of labeled training QRS complexes. Sparse representations, based on the designed dictionaries, of each new test QRS complex are then calculated. Its class is finally predicted using the winner-takes-all principle; that is, the class associated with the highest GI is chosen. Our experiments showed promising results for the classification of premature ventricular contractions using a patient-specific approach. For many of the subjects considered, our classifier attained accuracies close to 100 % on the test set.
Examining the Effects of Deer Antler Velvet Supplementation on Muscular Strength, Performance, and Markers of Delayed Onset Muscle Soreness.

Purpose: To examine the effects of deer antler velvet on muscular strength, performance, and markers of delayed onset muscle soreness following a 10-week resistance training period. Participants: 16 resistance-trained males (18-35) volunteered. Measures: DEXA, 1-RM, a power test, and a 70% performance trial were measured. Creatine kinase and self-reported soreness levels were measured following an eccentric trial. Results: No pre-experimental significant differences existed between the groups for any of the variables measured. There were no significant differences between the groups regarding body composition, strength, muscular performance, or improvements in creatine kinase and soreness levels from pre to post-intervention. Both groups demonstrated significant (p Conclusions: Deer antler velvet does not improve muscle size, strength, or performance. Nor does it reduce markers of DOMS following a 10-week supplementation period.
Die Fledermaus: Regarding Optokinetic Contrast Sensitivity and Light-Adaptation, Chicks Are Mice with Wings

Background Through adaptation, animals can function visually under an extremely broad range of light intensities. Light adaptation starts in the retina, through shifts in photoreceptor sensitivity and kinetics plus modulation of visual processing in retinal circuits. Although considerable research has been conducted on retinal adaptation in nocturnal species with rod-dominated retinas, such as the mouse, little is known about how cone-dominated avian retinas adapt to changes in mean light intensity. Methodology/Principal Findings We used the optokinetic response to characterize contrast sensitivity (CS) in the chick retina as a function of spatial frequency and temporal frequency at different mean light intensities. We found that: 1) daytime, cone-driven CS was tuned to spatial frequency; 2) nighttime, presumably rod-driven CS was tuned to temporal frequency and spatial frequency; 3) daytime, presumably cone-driven CS at threshold intensity was invariant with temporal and spatial frequency; and 4) daytime photopic CS was invariant with clock time. Conclusion/Significance Light- and dark-adaptational changes in CS were investigated comprehensively for the first time in the cone-dominated retina of an avian, diurnal species. The chick retina, like the mouse retina, adapts by using a “day/night” or “cone/rod” switch in tuning preference during changes in lighting conditions. The chick optokinetic response is an attractive model for noninvasive, behavioral studies of adaptation in retinal circuitry in health and disease.
Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem1[C]

The functional soil microbiome is an important parameter in developing a sustainable and effective strategy to increase crop yield and food security. There is considerable evidence in the literature that beneficial rhizospheric microbes can alter plant morphology, enhance plant growth, and increase mineral content. Of late, there is a surge to understand the impact of the microbiome on plant health. Recent research shows the utilization of novel sequencing techniques to identify the microbiome in model systems such as Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). However, it is not known how the community of microbes identified may play a role to improve plant health and fitness. There are very few detailed studies with isolated beneficial microbes showing the importance of the functional microbiome in plant fitness and disease protection. Some recent work on the cultivated microbiome in rice (Oryza sativa) shows that a wide diversity of bacterial species is associated with the roots of field-grown rice plants. However, the biological significance and potential effects of the microbiome on the host plants are completely unknown. Work performed with isolated strains showed various genetic pathways that are involved in the recognition of host-specific factors that play roles in beneficial host-microbe interactions. The composition of the microbiome in plants is dynamic and controlled by multiple factors. In the case of the rhizosphere, temperature, pH, and the presence of chemical signals from bacteria, plants, and nematodes all shape the environment and influence which organisms will flourish. This provides a basis for plants and their microbiomes to selectively associate with one another. This Update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.
Prevalence and Demographic Correlates of Overweight, Physical Activity, and Screen Time Among School-Aged Children in Urban China: The Shanghai Study

This study reports the prevalence and demographic correlates of overweight, as well as meeting physical activity and screen time guidelines, in Chinese children. A representative sample of school-aged children (n = 49 549) in Shanghai were participants. Children’s anthropometrics were objectively measured; their physical activity and screen time, and demographic variables including age, sex, skill proficiency, sport affiliation, and transportation mode were self-reported. Multivariate logistic regression analyses were conducted. The prevalence of overweight was 24.9%, meeting physical activity guidelines was 20.5%, and meeting screen time guidelines was 73.5%. Boys (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.50-1.71) had higher overweight prevalence than girls. Girls (OR = 0.91, 95% CI = 0.85-0.97) and those without sport affiliation (OR = 0.48, 95% CI = 0.42-0.54) were less likely to meet physical activity recommendations than their counterparts. Girls were more likely than boys to meet screen time recommendations (OR = 1.29, 95% CI = 1.22-1.37). Children’s sex, sport affiliation, and skill proficiency are factors that policymakers can use to improve body weight status, physical activity participation, and screen time.