Miracle-dz/UniFAR-FTUs huggingface dataset:
Patient‐centered care and genomic medicine: A qualitative provider study in the military health system

The diagnostic and predictive information produced by genomic sequencing may impact medical management, and it is critical that providers and institutions are able to use this information appropriately for patient care. Guided by the patient‐centered care model, we investigated provider perspectives of patient, provider, and system‐level factors that could influence the implementation of genomic medicine within the integrated healthcare system of the US Department of Defense (DOD). The purpose of this study was to explore patient‐centered care elements related to the application of genomic sequencing in a military healthcare facility to understand the current capability and key gaps for patient‐centered genomic medicine. Twenty DOD healthcare providers were interviewed regarding their past experiences and future expectations of genetics and genomics. These semi‐structured interviews were recorded, transcribed and analyzed. All providers interviewed had some experience with genetics, but the level of experience varied greatly. Providers reported widely differing degrees of knowledge and confidence regarding genetics and about military‐specific policies regarding genetics which varied by specialty. In addition, most providers stated that their department did not currently have the infrastructure to allow for the care of patients with secondary genetic findings, defined as genetic findings which are intentionally examined because of their importance to healthcare management, but are unrelated to the reason the individual underwent sequencing. This study reveals gaps in key elements of patient‐centered care related to genomic medicine that may be helpful to address in future implementation efforts.
First Case of Trueperella bernardiae Bacteremia in an Immunocompromised Patient in Korea

Dear Editor, Trueperella spp. are facultative anaerobic gram-positive bacilli usually found in the mammalian genital tract [1]. Of the five Trueperella spp. , T. bernardiae and T. pyogenes have been isolated in human clinical specimens [2, 3]. T. bernardiae has been reported as an opportunistic pathogen in chronic osteitis, prosthetic joint infection, and brain abscess cases [4-6]. However, bloodstream infections caused by T. bernardiae have been reported in only a few cases, mostly in immunocompromised patients [7, 8]. We report the first case of T. bernardiae bacteremia in Korea. The Institutional Review Board for Human Research, Yonsei University, Severance Hospital, Seoul, Korea, approved this study (approval number: 4-2019-0343) and waived the need for informed consent. An 83-year old woman with a history of diabetes mellitus, cerebrovascular disease, and paroxysmal atrial fibrillation was transferred to the emergency room at Severance Hospital from a geriatric hospital because of uncontrolled fever and hypotension in August 2016. Three days prior to admission, she had been treated with fluoroquinolone (200 mg, twice a day) in the geriatric hospital because of a Klebsiella pneumoniae urinary tract infection. In the emergency room, her mean blood pressure was 42 mmHg, heart rate was 58 beats/minutes, and body temperature was 35.8°C. Laboratory tests showed a blood leukocyte count of 14.73×10/L, neutrophil count of 13.04×10/L (88.5% of total leukocyte count), C-reactive protein (CRP) level of 1,668.57 nmol/L, and procalcitonin level of 3.91 μg/L. As K. pneumoniae septic shock was suspected, empirical antimicrobial treatment with meropenem was initiated. Ten milliliter of blood were collected in three sets of culture vials, including BacT/Alert FA Plus (bioMérieux, Marcy-l’Étoile, France) and BacT/Alert FN Plus (bioMérieux), which were incubated in a BacT/ALERT 3D automated blood culture system (bioMérieux) immediately. After four-day incubation, positive signals for bacterial growth were identified in two FA and two FN culture vials. Gram-positive cocci and gram-positive bacilli were observed on the smear preparation from the positive-signal culture vials. Following subculturing on blood agar, white, medium-sized colonies and grayish, pinpoint colonies were observed. The bacterial species were identified as S. aureus (identification log score: 2.163) and T. bernardiae (identification log score: 1.981), respectively, using a Bruker Biotyper matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system (Bruker Daltonics, Bremen, Germany). Because of the low identification log score (under 2.0) for the latter isolate, indicating correct identification at the genus level, the 1,366 bp 16S rRNA gene was sequenced by Sanger sequencing and compared with the ezBiocloud database (https://www.ezbiocloud.net/identify). This showed 99.85%
IPEM Topical Report: A 2018 IPEM survey of MRI use for external beam radiotherapy treatment planning in the UK

The benefits of integrating MRI into the radiotherapy pathway are well published, however there is little consensus in guidance on how to commission or implement its use. With a view to developing consensus guidelines for the use of MRI in external beam radiotherapy (EBRT) treatment planning in the UK, a survey was undertaken by an Institute of Physics and Engineering in Medicine (IPEM) working-party to assess the current landscape of MRI use in EBRT in the UK. A multi-disciplinary working-party developed a survey to understand current practice using MRI for EBRT treatment planning; investigate how MRI is currently used and managed; and identify knowledge gaps. The survey was distributed electronically to radiotherapy service managers and physics leads in 71 UK radiotherapy (RT) departments (all NHS and private groups). The survey response rate was 87% overall, with 89% of NHS and 75% of private centres responding. All responding centres include EBRT in some RT pathways: 94% using Picture Archiving and Communication System (PACS) images potentially acquired without any input from RT departments, and 69% had some form of MRI access for planning EBRT. Most centres reporting direct access use a radiology scanner within the same hospital in dedicated (26%) or non-dedicated (52%) RT scanning sessions. Only two centres reported having dedicated RT MRI scanners in the UK, lower than reported in other countries. Six percent of radiotherapy patients in England (data not publically available outside of England) have MRI as part of their treatment, which again is lower than reported elsewhere. Although a substantial number of centres acquire MRI scans for treatment planning purposes, most centres acquire less than five patient scans per month for each treatment site. Commissioning and quality assurance of both image registration and MRI scanners was found to be variable across the UK. In addition, staffing models and training given to different staff groups varied considerably across the UK, reflecting the current lack of national guidelines. The primary barriers reported to MRI implementation in EBRT planning included costs (e.g. lack of a national tariff for planning MRI), lack of MRI access and/or capacity within hospitals. Despite these challenges, significant interest remains in increasing MRI-assisted EBRT planning over the next five years.
Surface Mesh Segmentation and Reconstruction with Smooth Boundary Curves

In mesh segmentation for industrial design objects, each segment deﬁned by a region with closed boundary should correspond to its underlying surface constructed according to the designer’s intention. In order to generate those segments from the scanned data, we propose a method in which (i) more suitable regions are extracted by the region splitting/merging processing with a new splitting scheme from the obtained clusters, (ii) smooth and consistent boundaries are generated as intersection or contacting curves between the adjacent underlying surfaces, and (iii) the region is reconstructed with high-quality triangle facets. We demonstrate the effectiveness of our method by applying it to the scanned data of the real-world industrial design objects.
Platelet microRNA expression and association with platelet maturity and function in patients with essential thrombocythemia

Abstract Essential thrombocythemia (ET) is characterized by persistently elevated platelet counts and an increased risk of thromboembolic events. Dysregulated expression of small noncoding microRNAs (miRNAs) have been shown in ET and may influence platelet maturity and function in ET patients. In this study, we included 22 ET patients and 19 healthy controls to investigate the expression of 12 platelet miRNAs previously reported to be dysregulated in ET. Further, we investigated the correlation between the expression of selected miRNAs and platelet maturity and platelet function. Total RNA was isolated from platelets, and expression analyses were performed using TaqMan quantitative PCR (qPCR). Mean platelet volume (MPV) and immature platelet count and -fraction (IPC and IPF) were measured using the Sysmex XE-5000 automated haematology system. Platelet function was investigated by multiple electrode aggregometry (agonists: arachidonic acid (AA), thrombin-receptor-activating-peptide (TRAP) and adenosine diphosphate (ADP)), while platelet activation was determined by multi-colour flow cytometry (antibodies: bound-fibrinogen, CD63 and P-selectin (CD62p), agonists: AA, TRAP and ADP). We showed that miR-9 and miR-490 were significantly upregulated in ET patients compared with healthy controls (p-values < 0.01), while miR-10a, miR-28, miR-126, miR-155, miR-221, miR-222, miR-223 and miR-431 were significantly downregulated in ET patients (all p-values < 0.001). A significant positive correlation was observed between miR-431 and MPV, IPC and IPF (all p-values < 0.05). The expression of miR-126 was negatively correlated with platelet aggregation induced by AA and TRAP (p < 0.05). In addition, we found the expression of miR-9 and miR-490 to be negatively correlated with the percentage of fibrinogen-, CD63- and P-selectin- positive platelets using TRAP as agonist (p < 0.05). In conclusion, our data indicate that platelet microRNAs may play a role in ET and that specific microRNAs are correlated with platelet maturity and platelet function.
Strong Wet and Dry Adhesion by Cupped Microstructures

Recent advances in bio-inspired microfibrillar adhesives have resulted in technologies that allow reliable attachment to a variety of surfaces. Because capillary and van der Waals forces are considerably weakened underwater, fibrillar adhesives are however far less effective in wet environments. Although various strategies have been proposed to achieve strong reversible underwater adhesion, strong adhesives that work both in air and underwater without additional surface treatments have yet to be developed. In this study, we report a novel design—cupped microstructures (CM)—that generates strong controllable adhesion in air and underwater. We measured the adhesive performance of cupped polyurethane microstructures with three different cup angles (15, 30, and 45°) and the same cup diameter of 100 μm in dry and wet conditions in comparison to standard mushroom-shaped microstructures (MSMs) of the same dimensions. In air, 15°CM performed comparably to the flat MSM of the same size with an adhesion strength (force per real contact area) of up to 1.3 MPa, but underwater, 15°CM achieved 20 times stronger adhesion than MSM (∼1 MPa versus ∼0.05 MPa). Furthermore, the cupped microstructures exhibit self-sealing properties, whereby stronger pulls lead to longer stable attachment and much higher adhesion through the formation of a better seal.
Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties

SUMMARY A critical step in comparative genomics is the identification of differences in the presence/absence of encoded biochemical pathways among organisms. Our library, Pygenprop, facilitates these comparisons using data from the Genome Properties database. Pygenprop is written in Python and, unlike existing libraries, it is compatible with a variety of tools in the Python data science ecosystem, such as Jupyter Notebooks for interactive analyses and scikit-learn for machine learning. Pygenprop assigns YES, NO, or PARTIAL support for each property based on InterProScan annotations of open reading frames from an organism's genome. The library contains classes for representing the Genome Properties database as a whole and methods for detecting differences in property assignments between organisms. As the Genome Properties database grows, we anticipate widespread adoption of Pygenprop for routine genome analyses and integration within third-party bioinformatics software. AVAILABILITY AND IMPLEMENTATION Pygenprop is written in Python and is compatible with versions 3.6 or higher. Source code is available under Apache Licence Version 2 at https://github.com/Micromeda/pygenprop. The package can be installed from both PyPi (https://pypi.org/project/pygenprop/) and Anaconda (https://anaconda.org/lbergstrand/pygenprop). Documentation is available on Read the Docs (http://pygenprop.rtfd.io/).
Auditory Brainstem Responses in Children with Auditory Processing Disorder

Abstract Background: The ASHA recommends including electrophysiological measures in an auditory processing disorder (APD) assessment battery, but few audiologists do so, potentially because of limited published evidence for its utility. Purpose: This study compared the auditory brainstem responses (ABRs) of children with APD with age-matched children and adults. Study Sample: This study retrospectively examined the records of 108 children suspected of APD (sAPD) who had click-evoked ABRs recorded as part of their clinical assessment. Twenty adults and 22 typically developing (TD) children were recruited as controls. Data collection and Analysis: Click-evoked ABRs were recorded at slow (13.3 clicks/sec) and faster (57.7 clicks/sec) stimulation rates. ABRs were analyzed using typical clinical measures (latencies and interpeak intervals for waves I, III, and V) and using a model proposed by Ponton et al that offered a more detailed analysis of axonal conduction time and synaptic transmission delay. Results: Both clinical measures and the Ponton model analysis showed no significant differences between TD children and adults. Children sAPD showed absolute latencies that were significantly prolonged when compared with adults but not when compared with TD children. But individual children sAPD showed clinically significant delays (>2 standard deviations of TD children’s data). Examination of responses delineating axonal versus synaptic transmission showed significant delays in synaptic transmission in the group of children sAPD in comparison to TD children and adults. These results suggest that a significant portion of children with listening difficulties showed evidence of reduced or atypical brainstem functioning. Examining the responses for axonal and synaptic delays revealed evidence of a synaptic pattern of abnormalities in a significant portion (37.03%) of children sAPD. Such observations could provide objective evidence of factors potentially contributing to listening difficulties that are frequently reported in children identified with APD. Conclusions: Children sAPD often showed abnormalities in the ABR, suggesting a neurophysiologic origin of their reported difficulties, frequently originating at or before the first synapse. This study provides supportive evidence for the value of click-evoked ABRs in comprehensive auditory processing assessment batteries.
Impact of therapeutic modalities on disease-specific survival in older adults with glioblastoma: A single-institution retrospective cohort study

The standard first-line therapy for glioblastoma consists of maximal surgical resection, followed by concurrent chemoradiotherapy. Optimal management for older glioblastoma patients is unknown as they have not been extensively studied in clinical trials. We report data from a series of 156 consecutive glioblastoma patients treated at our institution from 2007 to 2017. Compared to glioblastoma patients aged 70 or less, the patients older than 70 were less likely to undergo surgical resection (34% vs. 64%; p = 0.0003), be treated with adjuvant chemotherapy (37% vs. 59%; p = 0.01) or radiation therapy (36% vs. 56%; p = 0.03). Disease-specific survival was significantly shorter in this age group (4.7 vs. 15.3 months; p = 0.002). Nonetheless, when older patients did undergo surgery or chemotherapy, the proportional improvement in cancer-specific survival was similar to the one recorded in younger patients, which is concordant with the findings of other published reports. A multidisciplinary input from neurosurgeons, medical and radiation oncologists, oncology pharmacists and geriatricians remain paramount for the optimal management of glioblastoma in patients older than 70.
A minimally invasive abdominal and left thoracic approach as a palliative treatment for adenocarcinoma of the esophagogastric junction with severe stenosis: A case report

We report a novel technique for combined laparoscopy and thoracoscopy for far‐advanced adenocarcinoma of the esophagogastric junction (AEG). A 56‐year‐old man presented with far‐advanced AEG, and an esophagogastroduodenoscopy revealed a type 2 lesion that encircled the esophagogastric junction. CT revealed stenosis of the esophagogastric junction, suspected invasion into the left side of the diaphragm, and lymph node metastases in the abdomen. We diagnosed Siewert type II AEG (cT4aN1M0, cStage IIIA) according to the Japanese Classification of Gastric Carcinoma, version 14. Laparoscopic and thoracoscopic proximal gastrectomy and lower esophagectomy with double‐tract reconstruction were performed as a palliative resection via a minimally invasive abdominal and left thoracic approach. However, localized peritoneal dissemination was detected. The patient was discharged with no postoperative morbidity. Hence, a minimally invasive abdominal and left thoracic approach provides good visualization, and it is safe for lower esophageal transection and intrathoracic anastomosis in the treatment of locally advanced AEG invading the surrounding tissues.
Informal caregivers in stroke: Life impact, support, and psychological well-being—A Swedish Stroke Register (Riksstroke) study

Background Informal caregivers provide a large amount of day-to-day assistance and are crucial for the ability of survivors to recover and adapt to life after stroke. Aim The development of caregiver support programs is limited by lack of large long-term follow-up studies. We present a comprehensive study of Swedish stroke caregivers' life situation in relation to degree of functional dependency of the survivor. Patients and methods In 2016, the Swedish Stroke Register, Riksstroke, conducted a long-term follow-up survey on caregivers to patients with stroke three and five years earlier. Items on psychological well-being were adapted from the 36-item short-form health survey and poor outcome was defined using the 36-item short-form health survey reference material. Survivor degree of dependency was indicated by the caregiver as independent, partially dependent, or completely dependent. Results A total of 5063 community dwelling dyads were included: 56.5% of survivors were independent, 33.4% partially dependent, and 10.1% completely dependent. Caregiver life impact, need of support, and proportion of poor psychological well-being increased incrementally with survivor degree of dependency. In the completely dependent group where 41.1% of survivors could not be left unattended for more than 1 h, 23.7% of caregivers expressed unmet need of caregiver support; 51.4% reported poor psychological well-being compared to 19.3% in the independent group. Conclusion The caregiver situation varies greatly with degree of survivor dependency which makes generalizations of caregiver needs difficult. Our results emphasize the need for integrating support aimed specifically at caregivers to survivors of stroke with a large degree of dependency.
A Multi-Answer Character Recognition Method and Its Implementation on a High-Performance Computing Cluster

In this paper, we present our work in the implementation and performance optimization of a novel multi-answer character recognition method on a highperformance computing cluster. The main algorithm used in this method is called the Brain-State-in-a-Box (BSB), which is an auto-associative neural network model. We applied optimization techniques on different parts of the BSB algorithm to improve the overall computing and communication performance of the system. Furthermore, the proposed method adopts a new way to train, recall, and organize the BSB models for different characters, in order to provide a sorted (based on recall convergence speed) list of candidates for a given character image.
Efficient Adsorption of Lead (II) from Aqueous Phase Solutions Using Polypyrrole-Based Activated Carbon

In this study, polypyrrole-based activated carbon was prepared by the carbonization of polypyrrole at 650 °C for 2 h in the presence of four-times the mass of KOH as a chemical activator. The structural and morphological properties of the product (polypyrrole-based activated carbon (PPyAC4)), analyzed by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and thermogravimetric analysis, support its applicability as an adsorbent. The adsorption characteristics of PPyAC4 were examined through the adsorption of lead ions from aqueous solutions. The influence of various factors, including initial ion concentration, pH, contact time, and adsorbent dose, on the adsorption of Pb2+ was investigated to identify the optimum adsorption conditions. The experimental data fit well to the pseudo-second-order kinetic model (R2 = 0.9997) and the Freundlich isotherm equation (R2 = 0.9950), suggesting a chemisorption pathway. The adsorption capacity was found to increase with increases in time and initial concentration, while it decreased with an increase in adsorbent dose. Additionally, the highest adsorption was attained at pH 5.5. The calculated maximum capacity, qm, determined from the Langmuir model was 50 mg/g.