Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of CT reconstruction algorithm on auto‐segmentation performance

Abstract Model‐based iterative reconstruction (MBIR) reduces CT imaging dose while maintaining image quality. However, MBIR reduces noise while preserving edges which may impact intensity‐based tasks such as auto‐segmentation. This work evaluates the sensitivity of an auto‐contouring prostate atlas across multiple MBIR reconstruction protocols and benchmarks the results against filtered back projection (FBP). Images were created from raw projection data for 11 prostate cancer cases using FBP and nine different MBIR reconstructions (3 protocols/3 noise reduction levels) yielding 10 reconstructions/patient. Five bony structures, bladder, rectum, prostate, and seminal vesicles (SVs) were segmented using an auto‐segmentation pipeline that renders 3D binary masks for analysis. Performance was evaluated for volume percent difference (VPD) and Dice similarity coefficient (DSC), using FBP as the gold standard. Nonparametric Friedman tests plus post hoc all pairwise comparisons were employed to test for significant differences (P < 0.05) for soft tissue organs and protocol/level combinations. A physician performed qualitative grading of 396 MBIR contours across the prostate, bladder, SVs, and rectum in comparison to FBP using a six‐point scale. MBIR contours agreed with FBP for bony anatomy (DSC ≥ 0.98), bladder (DSC ≥ 0.94, VPD < 8.5%), and prostate (DSC = 0.94 ± 0.03, VPD = 4.50 ± 4.77% (range: 0.07–26.39%). Increased variability was observed for rectum (VPD = 7.50 ± 7.56% and DSC = 0.90 ± 0.08) and SVs (VPD and DSC of 8.23 ± 9.86% range (0.00–35.80%) and 0.87 ± 0.11, respectively). Over the all protocol/level comparisons, a significant difference was observed for the prostate VPD between BSPL1 and BSTL2 (adjusted P‐value = 0.039). Nevertheless, 300 of 396 (75.8%) of the four soft tissue structures using MBIR were graded as equivalent or better than FBP, suggesting that MBIR offered potential improvements in auto‐segmentation performance when compared to FBP. Future work may involve tuning organ‐specific MBIR parameters to further improve auto‐segmentation performance. Running title: Impact of CT Reconstruction Algorithm on Auto‐segmentation Performance.
Acceptance and commitment therapy for breast cancer survivors with fear of cancer recurrence: A 3‐arm pilot randomized controlled trial

Fear of cancer recurrence (FCR) has a profound negative impact on quality of life (QOL) for many cancer survivors. Breast cancer survivors (BCS) are particularly vulnerable, with up to 70% reporting clinically significant FCR. To the authors' knowledge, evidence‐based interventions for managing FCR are limited. Acceptance and commitment therapy (ACT) promotes psychological flexibility in managing life's stressors. The current study examined the feasibility and preliminary efficacy of group‐based ACT for FCR in BCS.
Decision Support for Breast Cancer Detection: Classification Improvement Through Feature Selection

Several statistical-based approaches have been developed to support medical personnel in early breast cancer detection. This article presents a method for feature selection aimed at classifying cases into categories based on patients’ breast tissue measures and protein microarray. The effectiveness of this feature selection strategy was evaluated against the commonly used Wisconsin Breast Cancer Database—WBCD (with several patients and fewer features) and a new protein microarray data set (with several features and fewer patients). Features were ranked according to a feature importance index that combines parameters emerging from the unsupervised method of principal component analysis and the supervised method of Bhattacharyya distance. Observations of a training set were iteratively categorized into malignant and benign cases through 3 classification techniques: k-Nearest Neighbor, linear discriminant analysis, and probabilistic neural network. After each classification, the feature with the smallest importance index was removed, and a new categorization was carried out until there was only one feature left. The subset yielding maximum accuracy was used to classify observations in the testing set. Our method yielded average 99.17% accurate classifications in the testing set while retaining average 4.61 out of 9 features in the WBCD, which is comparable to the best results reported by the literature on that data set, with the advantage of relying on simple and widely available multivariate techniques. When applied to the microarray data, the method yielded average accuracy of 98.30% while retaining average 2.17% of the original features. Our results can aid health-care professionals during early diagnosis of breast cancer.
DNA barcoding of coastal ray-finned fishes in Vietnam

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.
Antigenic Variation of Avian Influenza A(H5N6) Viruses, Guangdong Province, China, 2014–2018

Market surveillance showed continuing circulation of avian influenza A(H5N6) virus in live poultry markets in Guangdong Province in 2017, despite compulsory vaccination for avian influenza A(H5Nx) and A(H7N9). We analyzed H5N6 viruses from 2014–2018 from Guangdong Province, revealing antigenic drift and decreased antibody response against the vaccine strain in vaccinated chickens.
Radiomics features of the primary tumor fail to improve prediction of overall survival in large cohorts of CT- and PET-imaged head and neck cancer patients

Radiomics studies require many patients in order to power them, thus patients are often combined from different institutions and using different imaging protocols. Various studies have shown that imaging protocols affect radiomics feature values. We examined whether using data from cohorts with controlled imaging protocols improved patient outcome models. We retrospectively reviewed 726 CT and 686 PET images from head and neck cancer patients, who were divided into training or independent testing cohorts. For each patient, radiomics features with different preprocessing were calculated and two clinical variables—HPV status and tumor volume—were also included. A Cox proportional hazards model was built on the training data by using bootstrapped Lasso regression to predict overall survival. The effect of controlled imaging protocols on model performance was evaluated by subsetting the original training and independent testing cohorts to include only patients whose images were obtained using the same imaging protocol and vendor. Tumor volume, HPV status, and two radiomics covariates were selected for the CT model, resulting in an AUC of 0.72. However, volume alone produced a higher AUC, whereas adding radiomics features reduced the AUC. HPV status and one radiomics feature were selected as covariates for the PET model, resulting in an AUC of 0.59, but neither covariate was significantly associated with survival. Limiting the training and independent testing to patients with the same imaging protocol reduced the AUC for CT patients to 0.55, and no covariates were selected for PET patients. Radiomics features were not consistently associated with survival in CT or PET images of head and neck patients, even within patients with the same imaging protocol.
Genetic platelet depletion is superior in platelet transfusion compared to current models

Genetically modified mice have advanced our knowledge on platelets in hemostasis and beyond tremendously. However, mouse models harbor certain limitations, including availability of platelet specific transgenic strains, and off-target effects on other cell types. Transfusion of genetically modified platelets into thrombocytopenic mice circumvents these problems. Additionally, ex vivo treatment of platelets prior to transfusion eliminates putative side effects on other cell types. Thrombocytopenia is commonly induced by administration of anti-platelet antibodies, which opsonize platelets to cause rapid clearance. However, antibodies do not differentiate between endogenous or exogenous platelets, impeding transfusion efficacy. In contrast, genetic depletion with the inducible diphtheria toxin receptor (iDTR) system induces thrombocytopenia via megakaryocyte ablation without direct effects on circulating platelets. We compared the iDTR system with antibody-based depletion methods regarding their utility in platelet transfusion experiments, outlining advantages and disadvantages of both approaches. Antibodies led to thrombocytopenia within two hours and allowed the dose-dependent adjustment of the platelet count. The iDTR model caused complete thrombocytopenia within four days, which could be sustained for up to 11 days. Neither platelet depletion approach caused platelet activation. Only the iDTR model allowed efficient platelet transfusion by keeping endogenous platelet levels low and maintaining exogenous platelet levels over longer time periods, thus providing clear advantages over antibody-based methods. Transfused platelets were fully functional in vivo, and our model allowed examination of transgenic platelets. Using donor platelets from already available genetically modified mice or ex vivo treated platelets, may decrease the necessity of platelet-specific mouse strains, diminishing off-target effects and thereby reducing animal numbers.
Wings as inertial appendages: how bats recover from aerial stumbles

ABSTRACT For many animals, movement through complex natural environments necessitates the evolution of mechanisms that enable recovery from unexpected perturbations. Knowledge of how flying animals contend with disruptive forces is limited, however, and is nearly nonexistent for bats, the only mammals capable of powered flight. We investigated perturbation recovery in Carollia perspicillata by administering a well-defined jet of compressed air, equal to 2.5 times bodyweight, which induced two types of disturbances, termed aerial stumbles: pitch-inducing body perturbations and roll-inducing wing perturbations. In both cases, bats responded primarily by adjusting extension of wing joints, and recovered pre-disturbance body orientation and left–right symmetry of wing motions over the course of only one wingbeat cycle. Bats recovered from body perturbations by symmetrically extending their wings cranially and dorsally during upstroke, and from wing perturbations by asymmetrically extending their wings throughout the recovery wingbeat. We used a simplified dynamical model to test the hypothesis that wing extension asymmetry during recovery from roll-inducing perturbations can generate inertial torques that alone are sufficient to produce the observed body reorientation. Results supported the hypothesis, and also suggested that subsequent restoration of symmetrical wing extension help to decelerate recovery rotation via passive aerodynamic mechanisms. During recovery, humeral elevation/depression remained largely unchanged while bats adjusted wing extension at the elbow and wrist, suggesting a proximo-distal gradient in the neuromechanical control of the wing. Highlighted Article: Bats rapidly recover from substantial disturbances to body orientation within one wingbeat, relying primarily upon inertial torques generated from left–right asymmetry in wingbeat kinematics.
Strong Vibrational Relaxation of NO Scattered from Au(111): Importance of the Adiabatic Potential Energy Surface.

Experimental observations of multi-quantum relaxation of highly vibrationally excited NO scattering from Au(111) are a benchmark for the breakdown of Born-Oppenheimer approximation in molecule-surface systems. This remarkable vibrational inelasticity was long thought to be almost exclusively mediated by electron transfer; but, no theories have quantitatively reproduced various experimental data. This was suggested to be due to errors in the adiabatic potential energy surface (PES) used in those studies. Here, we investigate electronically adiabatic molecular dynamics of this system with a globally accurate high dimensional PES, newly developed with neural networks from first principles. The NO vibrational energy loss is much larger than that on earlier adiabatic PES. Additionally, the translational inelasticity and translational energy dependence of vibrational inelasticity are also more accurately reproduced. There is reason to be optimistic that electronically nonadiabatic theories using this adiabatic PES as a starting point might accurately reproduce experimental results on this important system.
Experimental evidence that symbiotic bacteria produce chemical cues in a songbird

ABSTRACT Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here, we tested whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second experiment, we cultured bacteria from junco preen oil, and found that all of the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both experiments, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals. Summary: Experimental evidence shows that chemical cues relevant to reproductive behaviour in a songbird, the dark-eyed junco, are produced by bacteria associated with uropygial gland secretions.
Characteristics of prescription in 29 Level 3 Neonatal Wards over a 2-year period (2017-2018). An inventory for future research

Objectives The primary objective of this study is to determine the current level of patient medication exposure in Level 3 Neonatal Wards (L3NW). The secondary objective is to evaluate in the first month of life the rate of medication prescription not cited in the Summary of Product Characteristics (SmPC). A database containing all the medication prescriptions is collected as part of a prescription benchmarking program in the L3NW. Material and methods The research is a two-year observational cohort study (2017–2018) with retrospective analysis of medications prescribed in 29 French L3NW. Seventeen L3NW are present since the beginning of the study and 12 have been progressively included. All neonatal units used the same computerized system of prescription, and all prescription data were completely de-identified within each hospital before being stored in a common data warehouse. Results The study population includes 27,382 newborns. Two hundred and sixty-one different medications (International Nonproprietary Names, INN) were prescribed. Twelve INN (including paracetamol) were prescribed for at least 10% of patients, 55 for less than 10% but at least 1% and 194 to less than 1%. The lowest gestational ages (GA) were exposed to the greatest number of medications (18.0 below 28 weeks of gestation (WG) to 4.1 above 36 WG) (p<0.0001). In addition, 69.2% of the 351 different combinations of an medication INN and a route of administration have no indication for the first month of life according to the French SmPC. Ninety-five percent of premature infants with GA less than 32 weeks received at least one medication not cited in SmPC. Conclusion Neonates remain therapeutic orphans. The consequences of polypharmacy in L3NW should be quickly assessed, especially in the most immature infants.
Multiple disadvantage and major life events

A ‘major life event’ is any event that can have a substantial impact on a person’s wellbeing (Wilkins & Warren 2012). While these types of events are not necessarily regarded as negative, unwelcome or unexpected, they are generally accepted as having an impact nonetheless. They may also be perceived differently by each member of the household. Some of these events— such as births, deaths and marriages—are related to the normal human life cycle while others— such as the loss of a job, leading to possible financial hardship or social isolation—can be regarded as environmental stressors.
Is age more than manual material handling associated with lumbar vertebral body and disc changes? A cross-sectional multicentre MRI study

Objective Conflicting evidence exists to what extent manual material handling (MMH) causes lumbar disc disease, lack of evidence exist that this effect takes place especially at L5-S1 level, where the greatest moment occurs. The aim was to assess if lumbar vertebral body and disc changes are more common in people whose job involves significant MMH and, if so, to evaluate if lumbar vertebral body and disc changes are more prevalent in the lower part of the lumbar spine (L4-L5 and L5-S1). Design Observational, cross-sectional, with quasi-random recruitment. Setting Outpatient radiology units of three large hospitals in northern (Bologna and Brescia) and southern (Bari) Italy. Participants 183 consecutive adult subjects (89 males, 94 females) aged 20–70 years referred by the general practitioner or a specialist for MRI of the lumbar spine. Primary and secondary outcome measures Neuroradiologists (blind to clinical assessment) evaluated the prevalence of intervertebral disc and vertebral body changes in standardised MRI examinations. History of personal and family musculoskeletal diseases and injuries, current and previous MMH at work and during leisure time were assessed by interview and self-administered questionnaire. Results Participants were classified according their occupational exposure to MMH. No association was found between MMH and vertebral body and intervertebral disc changes, whereas age over 45 years was consistently associated with more disc extension beyond the interspace changes, Pfirrmann changes, osteophytes and Modic changes: the association was statistically significant at the conventional 5% level. Conclusions Age, and not MMH, seems to primarily affect the presence of intervertebral disc changes; prospective studies are needed to better explore the relationship between MMH and the possible presence (and level) of lumbar vertebral body and/or disc changes.
Personal and Clinical Vaginal Lubricants: Impact on Local Vaginal Microenvironment and Implications for Epithelial Cell Host Response and Barrier Function.

BACKGROUND A majority of US women report past use of vaginal lubricants to enhance the ease and comfort of intimate sexual activities. Lubricants are also administered frequently in clinical practice. We sought to investigate if hyperosmolar lubricants are toxic to the vaginal mucosal epithelia. METHODS We tested a panel of commercially available lubricants across a range of osmolalities in human monolayer vaginal epithelial cell (VEC) culture and a robust 3-dimensional (3-D) VEC model. The impact of each lubricant on cellular morphology, cytotoxicity, barrier targets, and the induction of inflammatory mediators was examined. Conceptrol, containing nonoxynol-9, was used as a cytotoxicity control. RESULTS We observed a loss of intercellular connections, and condensation of chromatin, with increasing lubricant osmolality. EZ Jelly, K-Y Jelly, Astroglide, and Conceptrol induced cytotoxicity in both models at 24 hours. There was a strong positive correlation (r = 0.7326) between lubricant osmolality and cytotoxicity in monolayer VECs, and cell viability was reduced in VECs exposed to all the lubricants tested for 24 hours, except McKesson. Notably, select lubricants altered cell viability, barrier targets, and inflammatory mediators in 3-D VECs. CONCLUSIONS These findings indicate that hyperosmolar lubricants alter VEC morphology and are selectively cytotoxic, inflammatory, and barrier disrupting in the 3-D VEC model.
Teaching in the Global Society: Exploring an Educational Program in an International Setting from the Perspective of Graduate Students

1. Abstract A recent trend in higher education is the internationalization of university programs. This paper examines the experiences of postsecondary graduate students enrolled in literacy education courses in Barbados. The courses were based on a constructivist pedagogical approach to learning and the instructors were interested in the transferability of graduate education course work when teachers come from, and teach in, a different culture and context. The researchers developed a qualitative study to examine graduate teachers’ perceptions of the courses to determine which aspects were most instrumental in contributing to learner engagement and to resulting changes in their teaching practices. The findings provide valuable insights into graduate students’ conceptualizations of their educational experiences and also support the benefits of a constructivist approach in the teaching and learning process.