Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction

1 Salmonella, a genus of the Gram-negative family Enterobacteriaceae comprises a large, closely related group of important bacteria, whose nomenclature is complex (Brenner et al., 2000; Tindall et al., 2005). The American Society for Microbiology (ASM) and the Centres for Diseases Control Prevention (CDC) use a system based on recommendations from the World Health Organisation Collaborating Centre that recognizes two Salmonella species, Salmonella enterica and Salmonella bongori (Board 1999; Brenner et al., 2000). S. enterica, which is medically the more significant of the two species, is classified into six subspecies (enterica, salamae, arizonae, diarizonae, houtenae and indica) which are further divided into serovars based on the antigenicity of the LPS (O-antigen) and flagella (H-antigen). In total >2,500 serovars of S. enterica have been described. Host range and virulence varies greatly between the different serovars (Coburn et al., 2007; Martins et al., 2013).
Stresses in the Cranial Cruciate Ligament Deficient Canine Stifle Following Three Tibial Osteotomy Procedures: A Finite Element Analysis.

CRIMI, CHRISTINA MARIE. Stresses in the Cranial Cru ciate Ligament Deficient Canine Stifle Following Three Tibial Osteotomy Procedures: A Finite Element Analysis. (Under the direction of Dr. Andre Mazzoleni and Dr. Ola Harrys son.) Cranial cruciate rupture remains one of the most wi dely diagnosed and threatening conditions to stifle stability and rear limb function in dogs. The objective of this research was to evaluate the post-operative effects of three common ly practiced corrective surgeries for a CCL deficient canine stifle. A fully three-dimensi onal, anatomically accurate, quasi-static, nonlinear computer model of the left hind limb of a healthy dog was analyzed via finite element analysis. This model was then modified to simulate CCL deficiency and subsequent treatment by means of three different surgical proc edures: the Tibial Plateau Leveling Osteotomy (TPLO), Tibial Tuberosity Advancement (TT A) and the Triple Tibial Osteotomy (TTO). Analysis was carried out for three stifle p ositions (75o, 113o, 148o) representing the normal range of motion of a large-breed dog. An in crease in stress on the CaCL was apparent in flexion and in good accordance with lit era ure and physical testing. The results of the models suggest that throughout the range of motion the TPLO increased the stress in the patellar ligament to a higher degree than did t he TTA or TTO. Additionally, the TTA appeared to increase the stress of the CaCL more th an the TPLO or TTO did at 75o of stifle flexion and, overall, the TTO resulted in a more co nsistent stress distribution. These results will give veterinary orthopedic surgeons a better u nderstanding of the effects of these procedures on the geometry and function of the cani ne stifle throughout a normal range of motion. Stresses in the Cranial Cruciate Ligament Deficient Canine Stifle Following Three Tibial Osteotomy Procedures: A Finite Element A alysis by Christina Marie Crimi A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements of the Degree of Master of Science Mechanical Engineering Raleigh, North Carolina 2008
Evaluation of image filters for their integration with LSQR computerized tomography reconstruction method

In CT (computerized tomography) imaging reconstruction, the acquired sinograms are usually noisy, so artifacts will appear on the resulting images. Thus, it is necessary to find the adequate filters to combine with reconstruction methods that eliminate the greater amount of noise possible without altering in excess the information that the image contains. The present work is focused on the evaluation of several filtering techniques applied in the elimination of artifacts present in CT sinograms. In particular, we analyze the elimination of Gaussian and Speckle noise. The chosen filtering techniques have been studied using four functions designed to measure the quality of the filtered image and compare it with a reference image. In this way, we determine the ideal parameters to carry out the filtering process on the sinograms, prior to the process of reconstruction of the images. Moreover, we study their application on reconstructed noisy images when using noisy sinograms and finally we select the best filter to combine with an iterative reconstruction method in order to test if it improves the quality of the images. With this, we can determine the feasibility of using the selected filtering method for our CT reconstructions with projections reduction, concluding that the bilateral filter is the filter that behaves best with our images. We will test it when combined with our iterative reconstruction method, which consists on the Least Squares QR method in combination with a regularization technique and an acceleration step, showing how integrating this filter with our reconstruction method improves the quality of the CT images.
Clinically significant changes in pain along the Pain Intensity Numerical Rating Scale in patients with chronic low back pain

Low back pain (LBP) is the most common cause of chronic pain. Numerous clinical scales are available for evaluating pain, but their objective criteria in the management of LBP patients remain unclear. This study aimed to determine an objective cutoff value for a change in the Pain Intensity Numerical Rating Scale (ΔPI-NRS) three months after LBP treatment. Its utility was compared with changes in six commonly used clinical scales in LBP patients: Pain Disability Assessment Scale (PDAS), Pain Self-Efficacy Questionnaire (PSEC), Pain Catastrophizing Scale (PCS), Athens Insomnia Scale (AIS), EuroQoL 5 Dimension (EQ5D), and Locomo 25. We included 161 LBP patients treated in two representative pain management centers. Patients were partitioned into two groups based on patient’s global impression of change (PGIC) three months after treatment: satisfied (PGIC = 1, 2) and unsatisfied (3–7). Multivariate logistic regression analysis was performed to explore relevant scales in distinguishing the two groups. We found ΔPI-NRS to be most closely associated with PGIC status regardless of pre-treatment pain intensity, followed by ΔEQ5D, ΔPDAS, ΔPSEC, and ΔPCS. The ΔPI-NRS cutoff value for distinguishing the PGIC status was determined by ROC analysis to be 1.3–1.8 depending on pre-treatment PI-NRS, which was rounded up to ΔPI-NRS = 2 for general use. Spearman’s correlation coefficient revealed close relationships between ΔPI-NRS and the six other clinical scales. Therefore, we determined cutoff values of these scales in distinguishing the status of ΔPI-NRS≥2 vs. ΔPI-NRS<2 to be as follows: ΔPDAS, 6.71; ΔPSEC, 6.48; ΔPCS, 6.48; ΔAIS, 1.91; ΔEQ5D, 0.08; and ΔLocomo 25, 9.31. These can be used as definitive indicator of therapeutic outcome in the management of chronic LBP patients.
Follow‐up of late‐onset Pompe disease patients with muscle magnetic resonance imaging reveals increase in fat replacement in skeletal muscles

Abstract Background Late‐onset Pompe disease (LOPD) is a genetic disorder characterized by progressive degeneration of the skeletal muscles produced by a deficiency of the enzyme acid alpha‐glucosidase. Enzymatic replacement therapy with recombinant human alpha‐glucosidase seems to reduce the progression of the disease; although at the moment, it is not completely clear to what extent. Quantitative muscle magnetic resonance imaging (qMRI) is a good biomarker for the follow‐up of fat replacement in neuromuscular disorders. The aim of this study was to describe the changes observed in fat replacement in skeletal muscles using qMRI in a cohort of LOPD patients followed prospectively. Methods A total of 36 LOPD patients were seen once every year for 4 years. qMRI, several muscle function tests, spirometry, activities of daily living scales, and quality‐of‐life scales were performed on each visit. Muscle MRI consisted of two‐point Dixon studies of the trunk and thigh muscles. Computer analysis of the images provided the percentage of muscle degenerated and replaced by fat in every muscle (known as fat fraction). Longitudinal analysis of the measures was performed using linear mixed models applying the Greenhouse–Geisser test. Results We detected a statistically significant and continuous increase in mean thigh fat fraction both in treated (+5.8% in 3 years) and in pre‐symptomatic patients (+2.6% in 3years) (Greenhouse–Geisser p < 0.05). As an average, fat fraction increased by 1.9% per year in treated patients, compared with 0.8% in pre‐symptomatic patients. Fat fraction significantly increased in every muscle of the thighs. We observed a significant correlation between changes observed in fat fraction in qMRI and changes observed in the results of the muscle function tests performed. Moreover, we identified that muscle performance and mean thigh fat fraction at baseline visit were independent parameters influencing fat fraction progression over 4 years (analysis of covariance, p < 0.05). Conclusions Our study identifies that skeletal muscle fat fraction continues to increase in patients with LOPD despite the treatment with enzymatic replacement therapy. These results suggest that the process of muscle degeneration is not stopped by the treatment and could impact muscle function over the years. Hereby, we show that fat fraction along with muscle function tests can be considered a good outcome measures for clinical trials in LOPD patients.
Early FDG-PET responses to PLX4032 in BRAF-mutant advanced melanoma.

8529 Background: FDG-PET is an effective imaging modality at assessing early response to a variety of agents that target key driver mutations in human cancer. Reduction in FDG uptake reflects inhibition of glycolytic metabolism and presumably rapid cell death and thus may provide early information on patient benefit. We aimed to determine the response rate using FDG-PET in patents with advanced melanoma treated with PLX4032 as defined by EORTC FDG-PET response criteria in target lesions in an international multicenter phase I study. Methods: Baseline and day 15 FDG PET were available in 22 pts with advanced metastatic melanoma treated at 3320mg BID. The cohort included 19 pts treated at 960mg BID, the MTD of PLX4032. As controls we analyzed 4 pts with advanced melanoma treated on the same study but at subtherapeutic doses (AUC uM*h 0-24 of 69±8, 25% reduction in SUVMax), with.
Commutative Properties of Head Direction Cells during Locomotion in 3D: Are All Routes Equal?

Navigation often requires movement in three-dimensional (3D) space. Recent studies have postulated two different models for how head direction (HD) cells encode 3D space: the rotational plane hypothesis and the dual-axis model. To distinguish these models, we recorded HD cells in female rats while they traveled different routes along both horizontal and vertical surfaces from an elevated platform to the top of a cuboidal apparatus. Navigation often requires movement in three-dimensional (3D) space. Recent studies have postulated two different models for how head direction (HD) cells encode 3D space: the rotational plane hypothesis and the dual-axis model. To distinguish these models, we recorded HD cells in female rats while they traveled different routes along both horizontal and vertical surfaces from an elevated platform to the top of a cuboidal apparatus. We compared HD cell preferred firing directions (PFDs) in different planes and addressed the issue of whether HD cell firing is commutative—does the order of the animal's route affect the final outcome of the cell's PFD? Rats locomoted a direct or indirect route from the floor to the cube top via one, two, or three vertical walls. Whereas the rotational plane hypothesis accounted for PFD shifts when the animal traversed horizontal corners, the cell's PFD was better explained by the dual-axis model when the animal traversed vertical corners. Responses also followed the dual-axis model (1) under dark conditions, (2) for passive movement of the rat, (3) following apparatus rotation, (4) for movement around inside vertical corners, and (5) across a 45° outside vertical corner. The order in which the animal traversed the different planes did not affect the outcome of the cell's PFD, indicating that responses were commutative. HD cell peak firing rates were generally equivalent along each surface. These findings indicate that the animal's orientation with respect to gravity plays an important role in determining a cell's PFD, and that vestibular and proprioceptive cues drive these computations. SIGNIFICANCE STATEMENT Navigating in a three-dimensional (3D) world is a complex task that requires one to maintain a proper sense of orientation relative to both local and global cues. Rodent head direction (HD) cells have been suggested to subserve this sense of orientation, but most HD cell studies have focused on navigation in 2D environments. We investigated the responses of HD cells as rats moved between multiple vertically and horizontally oriented planar surfaces, demonstrating that HD cells align their directional representations to both local (current plane of locomotion) and global (gravity) cues across several experimental conditions, including darkness and passive movement. These findings offer critical insights into the processing of 3D space in the mammalian brain.
CT images with expert manual contours of thoracic cancer for benchmarking auto-segmentation accuracy.

PURPOSE Automatic segmentation offers many benefits for radiotherapy treatment planning; however, the lack of publicly available benchmark datasets limits the clinical use of automatic segmentation. In this work, we present a well-curated CT dataset of high-quality manually drawn contours from patients with thoracic cancer that can be used to evaluate the accuracy of thoracic normal tissue auto-segmentation systems. ACQUISITION AND VALIDATION METHODS CT scans of 60 patients undergoing treatment simulation for thoracic radiotherapy were acquired from three institutions: MD Anderson Cancer Center, Memorial Sloan-Kettering Cancer Center, and the MAASTRO clinic. Each institution provided CT scans from 20 patients, including mean intensity projection (4D CT), exhale phase (4D CT), or free-breathing CT scans depending on their clinical practice. All CT scans covered the entire thoracic region with a 50-cm field of view and slice spacing of 1 mm, 2.5 mm, or 3 mm. Manual contours of left/right lungs, esophagus, heart, and spinal cord were retrieved from the clinical treatment plans. These contours were checked for quality and edited if necessary to ensure adherence to RTOG 1106 contouring guidelines. DATA FORMAT AND USAGE NOTES The CT images and RTSTRUCT files are available in DICOM format. The regions of interest were named according to the nomenclature recommended by AAPM Task Group 263 as Lung_L, Lung_R, Esophagus, Heart, and SpinalCord. This dataset is available on The Cancer Imaging Archive (funded by the National Cancer Institute) under Lung CT Segmentation Challenge 2017 (http://doi.org/10.7937/K9/TCIA.2017.3r3fvz08). POTENTIAL APPLICATIONS This dataset provides CT scans with well-delineated manually drawn contours from patients with thoracic cancer that can be used to evaluate auto-segmentation systems. Additional anatomies could be supplied in the future to enhance the existing library of contours.
Immunological and Disease Progression Virological Markers of HI

prognostic indicators for progression of HIV Janice M. Zelle~, PhD, RN, is Professor, Department of Medical Nursing, and Associate Professor, Department of immunology~Microbiology; and Nancy L. McCain, DSN, RN, is Associate Professor, School of Nursing Virginia Commonwealth University, Richmond, VA. Barbara Swanson, DNSc, RN, is Study Coordinator, Women's Interagency HIV Study, University of Illinois at Chicago.
Tenofovir alafenamide use in pregnant and lactating women living with HIV

ABSTRACT Introduction: Tenofovir alafenamide (TAF)-containing fixed-dose drug combinations (FDCs) are increasingly being used in managing pregnant women living with HIV. However, TAF is not currently recommended during pregnancy due to limited pharmacokinetic and safety data. TAF, a newer nucleotide phosphonamidate prodrug of tenofovir (TFV), achieves high levels of tenofovir-diphosphate in lymphoid cells and hepatocytes, and 90% lower systemic concentrations of TFV compared to tenofovir disoproxil fumarate (TDF), thereby maximizing TAF’s antiviral efficacy, potency and clinical safety. Areas covered: This review discusses the currently available information on the pharmacology of TAF in pregnant women living with HIV. Pharmacokinetic studies with TAF during pregnancy have yielded varying results compared to postpartum, but TAF exposures during pregnancy have been within the range of those typically observed in non-pregnant adults. The efficacy and safety of TAF in treatment-naïve pregnant women living with HIV is currently being evaluated in the VESTED study, a phase-III NIH randomized clinical trial. Expert opinion: Initial pregnancy data suggest that TAF-based FDCs have high efficacy and low risk of adverse effects during pregnancy. TAF is likely to become part of first-line regimens for use in pregnant women living with HIV once additional pregnancy data from phase III trials are available.
A spindle cell squamous cell carcinoma on the cheek presenting with in-transit metastases and a satellite lesion

Spindle cell squamous cell carcinoma (SpSCC) is a biphasic tumor composed of squamous cell epithelial and spindle cell mesenchymal components, both of which are malignant. Cutaneous SpSCC can cause diagnostic and therapeutic difficulties because of its rarity, heterogeneity, morphological similarity to other cutaneous spindle cell neoplasms, and uncertain pathogenesis and prognosis, particularly when the squamous cell carcinoma component is minimal or missing. Intransit metastasis and satellite lesion (satellitosis) constitute a spectrum of non-nodal regional metastases. Here the author reports the first known case of cutaneous SpSCC presenting with intransit metastases and a satellite lesion, which were exceptionally aggressive. A 77-year-old female patient presented with a 3× 3× 0.5 cm mass on her right cheek. Despite wide excision and postoperative radiation, the patient resulted in local recurrence and multiple distant metastases within 3 months. If many high-risk factors-particularly satellitosis and in-transit metastases are observed in a tumor with epithelial to mesenchymal transition, then further wide excision and adjuvant chemoradiation should be considered early in the treatment process. A multidisciplinary approach could be the key to cure the most aggressive malignancies of the skin, as in other organs.
Design of MINIX FS for Multi-Process Micro-Kernel Embedded OS on ARM

This paper describes the design and implementation of MINIX file system for an embedded OS in technical details, including an overview of MINIX FS, an introduction of the data structures for it, key techniques of implementing it, such as cache, foundational routines and interface functions. The file system is implemented on the multi-process micro-kernel embedded operating system on ARM, which is also designed by the author of this paper with GNU tool chain. The essential functions for a MINIX FS are accomplished, e.g. mount (), open (), close (), read (), write (), lseek (), unlink (), stat (), chdir (), mkdir (), rmdir (), execve (), etc. To show the effects of the file system, some related shell commands are also designed, e.g. cat, cp, echo, ls, pwd, etc. The file system is designed as simple as possible so that the code amount of it is only about 1,600 lines. With such a small scale, the system is suitable not only for embedded application system developments but also for embedded related curriculum teaching in colleges and universities.
Geographic Association Between Incidence of Acute Appendicitis and Socioeconomic Status.

Importance Some studies based on proportions of patients with perforated appendicitis (PA) among all patients with acute appendicitis (AA) have found an association between socioeconomic status (SES) and risk of perforation. A potential limitation is their use of proportions, which assumes that incidence of AA is evenly distributed across populations at risk. This assumption may be invalid, and SES may have a more complex association with both AA and PA. Objective To generate population-based incidences of AA and PA and to examine geographic patterns of incidence alongside geographic patterns of SES. Design, Setting, and Participants Retrospective study of data from Washington's Comprehensive Hospital Abstract Reporting System and the 2010 US census. Geographic methods were used to identify patterns of age- and sex-standardized incidence in Washington State between 2008 and 2012. The study included all patients discharged with International Classification of Diseases, Ninth Revision codes for AA or PA. Data were analyzed between November 2016 and December 2018. Exposures Location of primary residence. Main Outcomes and Measures Age- and sex-standardized incidence for AA and PA was generated for each census tract (CT). Global spatial autocorrelation was examined using Moran index (0.0 = completely random incidence; 1.0 = fully dependent on location). Clusters of low-incidence CTs (cold spots) and high-incidence CTs (hot spots) were identified for AA. Census-based SES data were aggregated for hot spots and cold spots and then compared. Results Statewide, over the 5-year study period, there were 35 730 patients with AA (including 9780 cases of PA), of whom 16 574 were women (46.4%). Median age of the cohort was 29 years (IQR, 16-48 years). Statewide incidence of AA and PA was 106 and 29 per 100 000 person-years (PY), respectively. Crude incidence was higher within the male population and peaked at age 10 to 19 years. Age- and sex-standardized incidence of AA demonstrated significant positive spatial autocorrelation (Moran index, 0.30; P < .001), but autocorrelation for PA was only half as strong (0.16; P < .001). Median incidence of AA was 118.1 per 100 000 PY among hot spots vs 86.2 per 100 000 PY among cold spots (P < .001). Socioeconomic status was higher in cold spots vs hot spots: mean proportion of college-educated adults was 56% vs 26% (P < .001), and mean per capita income was $44 691 vs $30 027 (P < .001). Conclusions and Relevance Age- and sex-standardized incidence of appendicitis is not randomly distributed across geographic subunits, and geographic clustering of AA is twice as strong as PA. Socioeconomic advantages, such as higher income and secondary education, are strongly associated with lower incidence of AA. These findings challenge conventional views that AA occurs randomly and has no predisposing characteristics beyond age/sex. Socioeconomic status, and likely other geographically circumscribed factors, are associated with incidence of AA.
Factors affecting antihypertensive medications adherence among hypertensive patients attending a general hospital in Jeddah City, Saudi Arabia

This research assessed factors affecting antihypertensive medication adherence among hypertensive patients in Saudi Arabia. It was a cross-sectional study that used a self-reporting method to identify the level of antihypertensive medication adherence and the contributing factors. The results of analysing the Hill-Bone Compliance scale revealed that 28% of the patients were optimal adherents and that 72% of the patients were suboptimal adherents to antihypertensive medications. The study has identified the following significant factors to be associated with antihypertensive medication adherence were patient’s concern about taking antihypertensive medication, their belief of the necessity of taking antihypertensive medications, and the patient-physician relationship. To our knowledge, this is the first study to identify the factors affecting antihypertensive treatment adherence in Saudi Arabia.