Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft Genome Sequence of Rhodococcus rhodochrous Strain G38GP, Isolated from the Madagascar Hissing Cockroach

Rhodococcus rhodochrous is a bacterial species with applications in biocatalysis and bioremediation. Here, we report the draft genome sequence of strain G38GP, isolated from the gut of the cockroach Gromphadorhina portentosa. The genome consists of 76 contigs, with a total length of 6,256,198 bp and a GC content of 67.82%. ABSTRACT Rhodococcus rhodochrous is a bacterial species with applications in biocatalysis and bioremediation. Here, we report the draft genome sequence of strain G38GP, isolated from the gut of the cockroach Gromphadorhina portentosa. The genome consists of 76 contigs, with a total length of 6,256,198 bp and a GC content of 67.82%.
Single-Molecule Junction Raman Spectroscopy on Distinct Metal-Molecule-Metal Systems

The understanding of electron transport through individual molecule species is fundamental in the field of molecular electronics. For example, molecular rectifiers, transistors, switches and amplifiers have been demonstrated. Herein the reliable control of electron transfer rates and loss mechanisms is highly important. In most cases, however, the detected parameter set is limited to the current-voltage (I-V) characteristic of single-molecule junctions. This thesis reports the combination of vibrational and electrical spectroscopy, employing a molecule junction spectroscopy (MJS) technique. For this purpose, a tetrahedral metal-coated glass tip was used as apertureless nearfield optics for Raman spectroscopy and simultaneously as counter electrode to a surface-anchored molecule. This allows recording Raman spectra concomitantly with the junction current as a function of the applied bias voltage. The first large part of this thesis was rebuilding and improving the MJS setup. Thereby, a higher stability, a significantly lower base pressure as well as a lower electric noise level was achieved. The optical investigation methods were upgraded by designing and implementing powerful routines. All experimental routines were implemented in LabVIEW. First, the feasibility of investigating a single-molecule at temperatures down to 77 K, using a gold-molecule-gold configuration, was demonstrated. Then the strain-induced change of the vibrational spectrum of a dithiol helicene molecule was investigated, revealing a red shift of the vibrational energy of a certain mode with increasing mechanical stress on the molecule. Finally, a ferromagnet-molecule-ferromagnet geometry was employed to observe the influence of the magnetic properties of the leads. These experiments show a negative differential conductance at a certain threshold voltage, which was accompanied by a change of the Raman signal. This effect was only observed in ferromagnetic junctions and could be explained by the formation of a spin valve.
Dose Rate Effects in Fluorescence Chemical Dosimeters Exposed to Picosecond Electron Pulses: An Accurate Measurement of Low Doses at High Dose Rates

The development of ultra-intense electron pulse for applications needs to be accompanied by the implementation of a practical dosimetry system. In this study four different systems were investigated as dosimeters for low doses with a very high-dose-rate source. First, the effects of ultra-short pulses were investigated for the yields of the Fricke dosimeter based on acidic solutions of ferrous sulfate; it was established that the yields were not significantly affected by the high dose rates, so the Fricke dosimeter system was used as a reference. Then, aqueous solutions of three compounds as fluorescence chemical dosimeters were utilized, each operated at a different solution pH: terephthalic acid - basic, trimesic acid - acidic, and coumarin-3-carboxylic acid (C3CA) - neutral. Fluorescence chemical dosimeters offer an attractive alternative to chemical dosimeters based on optical absorption for measuring biologically relevant low doses because of their higher sensitivity. The effects of very intense dose rate (TGy/ s) from pulses of fast electrons generated by a picosecond linear accelerator on the chemical yields of fluorescence chemical dosimeters were investigated at low peak doses (<20 Gy) and compared with yields determined under low-dose-rate irradiation from a 60 Co gamma-ray source (mGy/s). For the terephthalate and the trimesic acid dosimeters changes in the yields were not detected within the estimated (∼10%) precision of the experiments, but, due to the complexity of the mechanism of the hydroxyl radical initiated reactions in solutions of the relevant aromatic compounds, significant reductions of the chemical yield (–60%) were observed when the C3CA dosimeter was irradiated with the ultra-short pulses.
Trunk sway changes in professional bus drivers during actual shifts on long-distance routes

Abstract Although professional bus drivers are required to perform their task while adopting a prolonged constrained sitting posture, existence of possible effects in terms of postural strategies has been scarcely investigated under actual working conditions. This study aimed to characterise modifications of trunk sway in 14 professional bus drivers during regular shifts performed on non-urban routes using a pressure-sensitive mat placed on the seat. Centre-of-pressure (COP) time series were extracted from body-seat pressure data to calculate sway parameters (i.e. sway area, COP path length, COP displacements and velocities). Results show generalised increase in trunk sway as driving progresses, which becomes statistically significant after approximately 70–100 minutes of continuous driving. This may indicate the adoption of specific strategies to cope with discomfort onset or a fatigue-induced alteration of postural features. Trunk sway monitoring of bus drivers may be useful in detecting postural behaviours potentially associated with deteriorating performance and discomfort onset. Practitioner summary: Professional bus drivers operate in sitting position for prolonged time. Such constrained posture may induce discomfort and fatigue. We investigated trunk sway during actual shifts using pressure-sensitive mats. Significant increase of sway was detected after 70 min of continuous driving. Body-seat pressure data could be used as discomfort and fatigue markers. Abbreviations: ANOVA-RM: analysis of variance with repeated measures; AP: antero-posterior; COP: center of pressure; EC: ellipse’s centroid; ML: medio-lateral; SA: sway area; SP: sway path.
Letermovir prophylaxis in T-cell–depleted transplants: breakthrough and rebound infections in the postmarketing setting

We read with interest the recent article by Zamora et al describing that letermovir prophylaxis following allogeneic hematopoietic stem cell transplantation (allo-HSCT) may be associated with delayed reconstitution of cytomegalovirus (CMV)-speci ﬁ c T-cell immunity. 1
The mammalian rod synaptic ribbon is essential for Cav channel facilitation and ultrafast synaptic vesicle fusion

Rod photoreceptors (PRs) use ribbon synapses to transmit visual information. To signal ‘no light detected’ they release glutamate continually to activate post-synaptic receptors. When light is detected glutamate release pauses. How a rod’s individual ribbon enables this process was studied here by recording evoked changes in whole-cell membrane capacitance from wild-type and ribbonless (Ribeye-ko) mice. Wild-type rods filled with high (10 mM) or low (0.5 mM) concentrations of the Ca2+-buffer EGTA created a readily releasable pool (RRP) of 87 synaptic vesicles (SVs) that emptied as a single kinetic phase with a τ<0.4 ms. The lower concentration of EGTA accelerated Cav channel opening and facilitated release kinetics. In contrast, ribbonless rods created a much smaller RRP of 22 SVs, and they lacked Cav channel facilitation; however, Ca2+ channel-release coupling remained tight. These release deficits caused a sharp attenuation of rod-driven scotopic light responses. We conclude that the synaptic ribbon facilitates Ca2+-influx and establishes a large RRP of SVs.
Shear Wave Dispersion Imaging for the Characterization of Focal Liver Lesions – A Pilot study

Abstract Purpose Shear wave dispersion imaging is a novel ultrasound-based technique, which analyzes the speed of different shear wave components depending on their frequency. The dispersion of shear wave speed correlates with the viscosity of the liver parenchyma. The aim of this prospective study was to evaluate the use of shear wave dispersion imaging in focal liver lesions in the non-cirrhotic liver. Methods Patients with unclear focal liver lesions in B-mode ultrasound were prospectively assigned to shear wave dispersion imaging (m/s/kHz). Measurements were conducted within the lesion and in the liver parenchyma of the right liver lobe using an intercostal window. Histology and contrast-enhanced ultrasound served as the reference for the characterization of the lesions. Results Out of 46 patients included in this study, 24 had liver metastases and 22 had benign liver lesions. Benign lesions consisted mostly of hemangiomas (n=12) and focal nodular hyperplasia (n=8). Malignant lesions showed significantly lower shear wave dispersion (13.0±2.45 m/s/kHz) compared to benign tumors (15.2±2.74 m/s/kHz, p<0.01). In further subgroup analysis, the difference was significant for hemangiomas (15.32±2.42 m/s/kHz, p=0.04) but not for FNHs (14.98±3.36 m/s/kHz, p=0.38). The dispersion of reference liver parenchyma did not differ significantly between the groups (p=0.54). Conclusion The quantification of viscosity by shear wave dispersion is a new parameter for the characterization of focal liver lesions with higher dispersion values in hemangiomas and lower dispersion values in metastases. However, it cannot differentiate reliably between benign and malignant lesions.
Validation of the Child version of the Perseverative Thinking Questionnaire of repetitive negative thinking in young people with diagnosed depressive and anxiety disorders

This paper sought to provide the first validation of a transdiagnostic measure of repetitive negative thinking – the Perseverative Thinking Questionnaire‐Child version (PTQ‐C) – in young people diagnosed with anxiety and depressive disorders. Participants (N = 114) were 11‐ to 17‐year‐olds with complex and comorbid presentations seeking treatment through Child and Adolescent Mental Health Services. Confirmatory factor analyses best supported a three‐factor model for the PTQ‐C; however, hypotheses of both perfect and close fit were rejected, and a subsequent bifactor model suggested minimal unique variance for each subscale. Results demonstrated good internal consistency, convergent validity and divergent validity for the total score and three PTQ‐S subscales: core characteristics, perceived unproductiveness, and consumed mental capacity of negative repetitive thinking. PTQ‐C scores did not account for additional variance in anxiety symptoms once worry was considered, indicating that retention of a content‐specific measure may be warranted in clinical samples. Findings emphasize the importance of validating clinically relevant measures which were developed with subclinical populations in samples with diagnosed mental health disorders. Practitioner points Validates Perseverative Thinking Questionnaire in anxious and depressed youth. Support for convergent and divergent validity, and internal consistency. Results suggest measure is appropriate for complex and comorbid presentations.
Omission of sentinel node biopsy for breast cancer: Historical context and future perspectives on a modern controversy

For older patients with clinically lymph node‐negative breast cancer who have estrogen receptor‐positive tumors and are treated with tamoxifen, randomized trials comparing axillary lymph node dissection (ALND) versus no ALND show that the omission of ALND improves patient quality of life and has no adverse effects on mortality. These results have served to justify sentinel node biopsy (SNB) omission in selected older patients with breast cancer. More recently, clinical trials were launched to assess SNB omission in younger patients, with recurrence and survival as the primary outcomes of interest. Three important considerations serve as the basis for these ongoing trials. First, it is assumed that SNB omission will improve patient quality of life, although, to date, there is no level I evidence to support this assumption. Second, axillary surgery has never been shown to reduce breast cancer mortality, but it does reduce the risk of axillary recurrences, although adjuvant systemic therapy and radiotherapy also reduce these recurrence risks. Finally, nodal status is losing importance as a guide for adjuvant systemic therapy decision making because these decisions are now increasingly predicated on tumor biomarkers and gene profiling, but it is gaining importance for adjuvant radiotherapy decision making. Because quality‐of‐life considerations are the primary motivation for abandoning SNB, there is a need for randomized trials comparing SNB versus no SNB/no axillary surgery, with quality of life as the primary end point (level I evidence). Moreover, suitable alternatives to guide adjuvant radiotherapy decision making will require validation before SNB omission can be justified for patients of all ages who have clinically node‐negative breast cancer.
Single step zero-thermal-expansion temperature measurement of optical reference cavities.

State-of-the-art laser frequency stability has been pushed to the 10-17 level. The laser reference cavity is typically nested in a multi-layer thermal enclosure to increase vacuum thermal time constant and thermally controlled at the zero-thermal-expansion temperature to reduce the external temperature fluctuation effect. It is rather time consuming to accurately determine the zero-thermal-expansion temperature for a large thermal time constant system. Here we develop a fast method for measuring the zero-thermal-expansion temperature of the cavity by relying on just one single temperature scan. We first develop a theoretical model to predict the performance of the laser locked to the reference cavity, and then construct an evaluation system for verification of the model. The zero-thermal-expansion temperature of a 30-cm cavity is measured to be 4.3±0.5 °C. The fast and high precision method for determining the zero-thermal-expansion temperature will be valuable in improving long-term frequency stabilities of cavity stabilized lasers.
Virtual Reality–Based and Conventional Visual Field Examination Comparison in Healthy and Glaucoma Patients

Purpose Clinically evaluate the noninferiority of a custom virtual reality (VR) perimetry system when compared to a clinically and routinely used perimeter on both healthy subjects and glaucoma patients. Methods We use a custom-designed VR perimetry system tailored for visual field testing. The system uses Oculus Quest VR headset (Facebook Technologies, LLC, Bern, Switzerland), that includes a clicker for participant response feedback. A prospective, single center, study was conducted at the Department of Ophthalmology of the Bern University Hospital (Bern, Switzerland) for 12 months. Of the 114 participants recruited 70 subjects (36 healthy and 34 glaucoma patients with early to moderate visual field loss) were included in the study. Participants underwent perimetry tests on an Octopus 900 (Haag-Streit, Köniz, Switzerland) as well as on the custom VR perimeter. In both cases, standard dynamic strategy (DS) was used in conjunction with the G testing pattern. Collected visual fields (VFs) from both devices were then analyzed and compared. Results High mean defect (MD) correlations between the two systems (Spearman, ρ ≥ 0.75) were obtained. The VR system was found to slightly underestimate VF defects in glaucoma subjects (1.4 dB). No significant bias was found with respect to eccentricity or subject age. On average, a similar number of stimuli presentations per VF was necessary when measuring glaucoma patients and healthy subjects. Conclusions This study demonstrates that a clinically used perimeter and the proposed VR perimetry system have comparable performances with respect to a number of perimetry parameters in healthy and glaucoma patients with early to moderate visual field loss. Translational Relevance This suggests that VR perimeters have the potential to assess VFs with high enough confidence, whereby alleviating challenges in current perimetry practices by providing a portable and more accessible visual field test.
Building panoptic change segmentation with the use of uncertainty estimation in squeeze-and-attention CNN and remote sensing observations

ABSTRACT In conventional frameworks, the building change prediction of the deep model can be just blindly assumed accurate, but sometimes the truth is not. In this study, a new deep convolutional neural network (CNN) is proposed for building panoptic change segmentation using uncertainty estimation in squeeze-and-attention CNN and remote sensing observations. The setup is based on a large-scale dataset, called the LEVIR building change detection dataset (also known as LEVIR-CD), including bi-temporal red-green-blue (RGB) images labelled for building change segmentation with a period of 5 to 14 years have significant land-use changes from 20 various areas that sit in Texas of the United States. The quantitative assessments of the LEVIR-CD dataset show that the panoptic quality (PQ), recognition quality (RQ), segmentation quality (SQ), and mean intersection over union (mIoU) for building panoptic change segmentation are about 91.8, 94.7, 96.9, and 97.3, respectively. Compared with the deep learning networks with different backbones and loss functions, the proposed method demonstrates better performance and good generalization ability for building panoptic change segmentation.
The restoration of gotong royong as a form of post-disaster solidarity in Lombok, Indonesia

ABSTRACT This article explores the mobilization of local resources to reconstruct devastated villages in Lombok after the earthquake of 2018. Local leadership and NGOs managed to mobilize survivors and their communities to rebuild their devastated built environment by evincing the principle of gotong royong. They made an effort to include the survivors in the reconstruction effort, enabling them to begin their recovery trajectory and creating bonds of friendship and trust between various religious groups and villages. In other disaster aftermath situations, such as Aceh after the tsunami of 2004, NGOs and the Indonesian government did not succeed in mobilizing survivors by evoking the principle of gotong royong and, in some cases, even paralyzed the communities they tried to help. On the basis of qualitative data collected immediately after the earthquakes in 2018 and in the following year, I argue that local leaders and NGOs managed to mobilize these groups through effective leadership, transparency about funds and goals, stakeholder participation, an understanding of local legislature and explicit roles of accountability.
Advancements in satellite image classification : methodologies, techniques, approaches and applications

ABSTRACT Segmentation and classification are two imperative, yet challenging tasks in image analysis for remote-sensing applications. In the former, an image is divided into spatially continuous, disjoint, and homogeneous regions, called clusters, in terms of their various properties: shape, intensity, texture, colour, contrast, etc. Classification, on the other hand, is applied later in the process, to recognize or categorize individual objects or targets. Each task plays an important role in the refinement and enhancement of the various utilizations of remote sensing images. Driven by recent progress in earth observation sensor technology, satellite image classification systems for earth-observation applications have seen significant growth and progress. This growth has led to a notable increase in the number of published materials in these areas. We present an overview of the horizons that the modern remote sensing domain promises in terms of the efficient classification processing of satellite imagery. We begin by defining remote sensing, specifically in the context of its potential application areas, and highlight the importance of pre-processing and feature extraction steps’ in accurate classification. Various works have proposed novel segmentation, feature extraction/selection, and classification methods; these have been collected and duly reported in this work. The deep learning classification method has been given special attention due to its relatively limited dependence on training data, its wide spectrum of applications, and its ability to autonomously classify images with higher accuracy. We conclude by presenting a critical evaluation of the important contributions in this domain.
Review of Poultry Recombinant Vector Vaccines

SUMMARY. The control of poultry diseases has relied heavily on the use of many live and inactivated vaccines. However, over the last 30 yr, recombinant DNA technology has been used to generate many novel poultry vaccines. Fowlpox virus and turkey herpesvirus are the two main vectors currently used to construct recombinant vaccines for poultry. With the use of these two vectors, more than 15 recombinant viral vector vaccines against Newcastle disease, infectious laryngotracheitis, infectious bursal disease, avian influenza, and Mycoplasma gallisepticum have been developed and are commercially available. This review focuses on current knowledge about the safety and efficacy of recombinant viral vectored vaccines and the mechanisms by which they facilitate the control of multiple diseases. Additionally, the development of new recombinant vaccines with novel vectors will be briefly discussed.
Detection and Typing of a Fowl Adenovirus Type 1 Agent of Pancreatitis in Guinea Fowl

SUMMARY. Adenoviral pancreatitis has been amply described for decades in guinea fowl. Although its pathologic picture has been characterized fairly well, its etiology still remains only partially clarified. Based on several outbreaks diagnosed on commercial guinea flocks raised in France since 2017, we performed direct whole-genome sequencing from pancreatic lesional tissue by using the Oxford Nanopore Technologies (ONT) sequencing method. We generated 4781 viral reads and assembled a whole genome of 43,509 bp, clustering within fowl adenovirus type 1 (FAdV-1). A phylogenetic analysis based on a partial sequence of the hexon and short fiber genes on viruses collected in France showed 98.7% and 99.8% nucleotide identity, respectively. Altogether, these results confirm that an FAdV-1 closely related to chicken and other avian strains is the agent of pancreatitis in guinea fowl. This study illustrates the potential of ONT sequencing method to achieve rapid whole-genome sequencing directly from pathologic material.