Miracle-dz/UniFAR-FTUs huggingface dataset:
Image Segmentation of Operative Neuroanatomy Into Tissue Categories Using a Machine Learning Construct and Its Role in Neurosurgical Training

BACKGROUND: The complexity of the relationships among the structures within the brain makes efficient mastery of neuroanatomy difficult for medical students and neurosurgical residents. Therefore, there is a need to provide real-time segmentation of neuroanatomic images taken from various perspectives to assist with training. OBJECTIVE: To develop the initial foundation of a neuroanatomic image segmentation algorithm using artificial intelligence for education. METHODS: A pyramidal scene-parsing network with a convolutional residual neural network backbone was assessed for its ability to accurately segment neuroanatomy images. A data set of 879 images derived from The Neurosurgical Atlas was used to train, validate, and test the network. Quantitative assessment of the segmentation was performed using pixel accuracy, intersection-over-union, the Dice similarity coefficient, precision, recall, and the boundary F1 score. RESULTS: The network was trained, and performance was assessed class wise. Compared with the ground truth annotations, the ensembled results for our artificial intelligence framework for the pyramidal scene-parsing network during testing generated a total pixel accuracy of 91.8%. CONCLUSION: Using the presented methods, we show that a convolutional neural network can accurately segment gross neuroanatomy images, which represents an initial foundation in artificial intelligence gross neuroanatomy that will aid future neurosurgical training. These results also suggest that our network is sufficiently robust, to an unprecedented level, for performing anatomic category recognition in a clinical setting.
Bowel habits, faecal microbiota and faecal bile acid composition of healthy adults consuming fruit pomace fibres: two-arm, randomised, double-blinded, placebo-controlled trials

Abstract Dietary fibre modulates gastrointestinal (GI) health and function, providing laxation, shifting microbiota, and altering bile acid (BA) metabolism. Fruit juice production removes the polyphenol- and fibre-rich pomace fraction. The effects of orange and apple pomaces on GI outcomes were investigated in healthy, free-living adults. Healthy adults were enrolled in two double-blinded, crossover trials, being randomised by baseline bowel movement (BM) frequency. In the first trial, subjects (n 91) received orange juice (OJ, 0 g fibre/d) or OJ + orange pomace (OJ + P, 10 g fibre/d) for 4 weeks, separated by a 3-week washout. Similarly, in the second trial, subjects (n 90) received apple juice (AJ, 0 g fibre/d) or AJ + apple pomace (AJ + P, 10 g fibre/d). Bowel habit diaries, GI tolerance surveys and 3-d diet records were collected throughout. Fresh faecal samples were collected from a participant subset for microbiota and BA analyses in each study. Neither pomace interventions influenced BM frequency. At Week 4, OJ + P tended to increase (P = 0·066) GI symptom occurrence compared with OJ, while AJ + P tended (P = 0·089) to increase flatulence compared with AJ. Faecalibacterium (P = 0·038) and Negativibacillus (P = 0·043) were differentially abundant between pre- and post-interventions in the apple trial but were no longer significant after false discovery rate (FDR) correction. Baseline fibre intake was independently associated with several microbial genera in both trials. Orange or apple pomace supplementation was insufficient to elicit changes in bowel habits, microbiota diversity or BA of free-living adults with healthy baseline BM. Future studies should consider baseline BM frequency and habitual fibre intake.
Constrained Density Functional Theory: A Potential-Based Self-Consistency Approach

Chemical reactions, charge transfer reactions, and magnetic materials are notoriously difficult to describe within Kohn–Sham density functional theory, which is strictly a ground-state technique. However, over the last few decades, an approximate method known as constrained density functional theory (cDFT) has been developed to model low-lying excitations linked to charge transfer or spin fluctuations. Nevertheless, despite becoming very popular due to its versatility, low computational cost, and availability in numerous software applications, none of the previous cDFT implementations is strictly similar to the corresponding ground-state self-consistent density functional theory: the target value of constraints (e.g., local magnetization) is not treated equivalently with atomic positions or lattice parameters. In the present work, by considering a potential-based formulation of the self-consistency problem, the cDFT is recast in the same framework as Kohn–Sham DFT: a new functional of the potential that includes the constraints is proposed, where the constraints, the atomic positions, or the lattice parameters are treated all alike, while all other ingredients of the usual potential-based DFT algorithms are unchanged, thanks to the formulation of the adequate residual. Tests of this approach for the case of spin constraints (collinear and noncollinear) and charge constraints are performed. Expressions for the derivatives with respect to constraints (e.g., the spin torque) for the atomic forces and the stress tensor in cDFT are provided. The latter allows one to study striction effects as a function of the angle between spins. We apply this formalism to body-centered cubic iron and first reproduce the well-known magnetization amplitude as a function of the angle between local magnetizations. We also study stress as a function of such an angle. Then, the local collinear magnetization and the local atomic charge are varied together. Since the atomic spin magnetizations, local atomic charges, atomic positions, and lattice parameters are treated on an equal footing, this formalism is an ideal starting point for the generation of model Hamiltonians and machine-learning potentials, computation of second or third derivatives of the energy as delivered from density-functional perturbation theory, or for second-principles approaches.
White blood cell detection using saliency detection and CenterNet: A two‐stage approach

White blood cell (WBC) detection plays a vital role in peripheral blood smear analysis. However, cell detection remains a challenging task due to multi‐cell adhesion, different staining and imaging conditions. Owing to the powerful feature extraction capability of deep learning, object detection methods based on convolutional neural networks (CNNs) have been widely applied in medical image analysis. Nevertheless, the CNN training is time‐consuming and inaccuracy, especially for large‐scale blood smear images, where most of the images are background. To address the problem, we propose a two‐stage approach that treats WBC detection as a small salient object detection task. In the first saliency detection stage, we use the Itti's visual attention model to locate the regions of interest (ROIs), based on the proposed adaptive center‐surround difference (ACSD) operator. In the second WBC detection stage, the modified CenterNet model is performed on ROI sub‐images to obtain a more accurate localization and classification result of each WBC. Experimental results showed that our method exceeds the performance of several existing methods on two different data sets, and achieves a state‐of‐the‐art mAP of over 98.8%.
Use of Vitex doniana (black plum) and Abutilon hirtum (Florida keys) extracts as an integral part of phytomedicine in tackling multidrug-resistant Salmonella.

INTRODUCTION The high prevalence and global spread of antibiotic resistance is driving the search for new antibacterial agents. Screening small molecules against specific bacterial targets has not yielded new compounds therefore functional assays and phenotypic screens are now being used. In Nigeria, drug resistance towards Salmonella is a major public health concern. METHODOLOGY Nine fully characterized clinical Salmonella isolates, from the Department of Medical Microbiology, Jos University Teaching Hospital, Plateau State, Nigeria, were screened by broth microdilution for susceptibility to fractionated ethanol extracts of Vitex doniana and Abutilon hirtum. This was compared to the control organism ATCC25922 and a range antibiotics: CH (chloramphenicol), SP (sparfloxacin), AM (amoxicillin), CN (gentamicin), S (streptomycin), PEF (pefloxacin). RESULTS The most common resistance profile was AM,CN,S with most isolates susceptible to fluoroquinolones. Activity was detected from both plant extracts with MICs of extracted fractions ranging from 150 - 300 µg/mL. Interestingly both plants produced extracts with bactericidal activity from 300 - 600 µg/mL. V. doniana exhibited better activity against the resistant Salmonella strains in terms of greater inhibition zones, but A. hirtum extracts were more consistently active against all isolates. In comparison with the synthetic drugs, both plant extracts exhibited activity against more isolates - this activity was bactericidal. CONCLUSIONS Nigeria needs better anti-salmonella products and these results represent a starting point for antibiotic drug discovery.
Inline Tests

Unit tests are widely used to check source code quality, but they can be too coarse-grained or ill-suited for testing individual program statements. We introduce inline tests to make it easier to check for faults in statements. We motivate inline tests through several language features and a common testing scenario in which inline tests could be beneficial. For example, inline tests can allow a developer to test a regular expression in place. We also define language-agnostic requirements for inline testing frameworks. Lastly, we implement I-Test, the first inline testing framework. I-Test works for Python and Java, and it satisfies most of the requirements. We evaluate I-Test on open-source projects by using it to test 144 statements in 31 Python programs and 37 Java programs. We also perform a user study. All nine user study participants say that inline tests are easy to write and that inline testing is beneficial. The cost of running inline tests is negligible, at 0.007x–0.014x, and our inline tests helped find two faults that have been fixed by the developers.
Using 1991T/1999aa-like Type Ia Supernovae as Standardizable Candles

We present the photometry of 16 91T/99aa-like Type Ia Supernovae (SNe Ia) observed by the Las Cumbres Observatory. We also use an additional set of 21 91T/99aa-like SNe Ia and 87 normal SNe Ia from the literature for an analysis of the standardizability of the luminosity of 91T/99aa-like SNe. We find that 91T/99aa-like SNe are 0.2 mag brighter than normal SNe Ia, even when fully corrected by the light-curve shapes and colors. The weighted rms of the 91T/99aa-like SNe (with z CMB > 0.01) Hubble residuals is 0.25 ± 0.03 mag, suggesting that 91T/99aa-like SNe are also excellent relative distance indicators to ±12%. We compare the Hubble residuals with the pseudo-equivalent width (pEW) of Si ii λλ6355 around the date of maximum brightness. We find that there is a broken linear correlation between those two measurements for our sample including both 91T/99aa-like and normal SNe Ia. As the pEWmax (Si ii λλ6355) increases, the Hubble residual increases when pEWmax (Si ii λλ6355) < 55.6 Å. However, the Hubble residual stays constant beyond this. Given that 91T/99aa-like SNe possess shallower Si ii lines than normal SNe Ia, the linear correlation at pEWmax (Si ii λλ6355) < 55.6 Å can account for the overall discrepancy of Hubble residuals derived from the two subgroups. Such a systematic effect needs to be taken into account when using SNe Ia to measure luminosity distances.
Tensor Rank and Other Multipartite Entanglement Measures of Graph States

Graph states play an important role in quantum information theory through their connection to measurement-based computing and error correction. Prior work has revealed elegant connections between the graph structure of these states and their multipartite entanglement content. We continue this line of investigation by identifying additional entanglement properties for certain types of graph states. From the perspective of tensor theory, we tighten both upper and lower bounds on the tensor rank of odd ring states ( | R 2 n +1 (cid:105) ) to read 2 n + 1 ≤ rank( | R 2 n +1 (cid:105) ) ≤ 3 · 2 n − 1 . Next, we show that several multipartite extensions of bipartite entanglement measures are dichotomous for graph states based on the connectivity of the corresponding graph. Lastly, we give a simple graph rule for computing the n -tangle τ n .
One-Shot Doc Snippet Detection: Powering Search in Document Beyond Text

Active consumption of digital documents has yielded scope for research in various applications, including search. Traditionally, searching within a document has been cast as a text matching problem ignoring the rich layout and visual cues commonly present in structured documents, forms, etc. To that end, we ask a mostly unexplored question: "Can we search for other similar snippets present in a target document page given a single query instance of a document snippet? ". We propose MONOMER to solve this as a one-shot snippet detection task. MONOMER fuses context from visual, textual, and spatial modalities of snippets and documents to find query snippet in target documents. We conduct extensive ablations and experiments showing MONOMER outperforms several baselines from one-shot object detection (BHRL), template matching, and document understanding (LayoutLMv3). Due to the scarcity of relevant data for the task at hand, we train MONOMER on programmatically generated data having many visually similar query snippets and target document pairs from two datasets - Flamingo Forms and PubLayNet. We also do a human study to validate the generated data.
Humidity during high‐frequency oscillatory ventilation compared to intermittent positive pressure ventilation in extremely preterm neonates: An in vitro and in vivo observational study

Inappropriate humidification of inspired gas during mechanical ventilation can impair lung development in extremely low birthweight (ELBW) infants. Humidification depends on multiple factors, such as the heater‐humidifier device used, type of ventilation, and environmental factors. Few studies have examined inspired gas humidification in these infants, especially during high‐frequency oscillatory ventilation (HFOV). Our objective was to compare humidity during HFOV and intermittent positive pressure ventilation (IPPV), in vitro and in vivo.
Presepsin cut-off value for diagnosis of sepsis in patients with renal dysfunction

Presepsin is used as a marker for diagnosing sepsis, but its serum concentration is affected by renal function. We investigated the effect of the estimated glomerular filtration rate (eGFR) determined by creatinine on the diagnostic accuracy of presepsin to identify the optimal cut-off value in patients with renal dysfunction. A total of 834 patients aged ≥18 years with serum presepsin and creatinine measured on the same day over a period of 1 year were included. Sepsis was diagnosed in three ways: sepsis-1, sepsis-3, and clinical diagnosis (Sep-C). Presepsin showed a significant negative correlation with eGFR (r = −0.55, p<0.01), with median and interquartile ranges of presepsin values for patients in each eGFR category as follows: ≥90, 263 (169–460); ≥60–<90, 309 (205–578); ≥45–<60, 406 (279–683); ≥30–<45, 605 (379–1109); ≥15–<30, 1027 (675–1953); <15, 1977 (1199–3477); and on hemodialysis, 3964 (2343–6967). In receiver operating characteristic (ROC) analysis, the area under the curve (AUC) for sepsis-1 was the lowest (0.64 ± 0.02), while Sep-C (0.80± 0.03) and sepsis-3 (0.75 ± 0.03) were moderately accurate. Comparing AUCs after dividing patients into eGFR ≥60 and <60 showed that the AUC of Sep-C was lower in the eGFR ≥60 group, while the AUC of sepsis-3 was ≥ 0.7 in both groups. The following cut-offs were obtained by ROC analysis for sepsis-3: 466 pg/mL in the ≥60 group and 960 pg/mLin the < 60 group. Presepsin facilitated diagnosis sepsis based on sepsis-3 criteria regardless of renal function. We found that the optimal cut-offs for patients in this study were 500 pg/mL for eGFR ≥ 60 and 1000 pg/mL for < 60. However, future prospective diagnostic studies on sepsis-3 are needed to determine the cut-offs for patients with renal dysfunction.
Peptide epitopes as biomarkers of soya sensitization in rBet v 1 immunotherapy of birch‐related soya allergy

There are no diagnostic and/or prognostic markers of the treatment outcome in patients receiving allergen immunotherapy (AIT). Although numerous allergen epitopes are known, their value in this context has not been investigated. This paper deals with re‐evaluation of sera from patients who underwent AIT against rBet v 1 for treatment of their soya allergy (BASALIT trial).
NGO perspectives on the challenges and opportunities for real-world evaluation: a qualitative study

ABSTRACT Background The move towards robust monitoring and evaluation (M&E) has been increasing in global health, motivated by both an accountability agenda and to increase learning from M&E activities. Many international non-governmental organizations (NGOs) receive funding from one or more large institutional donors. Objective To understand NGOs’ perspective on their own role in terms of accountability to both donors and the populations they serve. Methods We conducted a series of in-depth interviews with M&E staff in 11 NGOs with projects related to maternal and child health to better understand how M&E is being implemented in these organizations. We then examined the data based on a priori identified themes. Results We found that despite flexibility from some donors, rigid reporting structures remain a barrier for NGOs to fully communicate the impact of their projects. While NGOs do utilize M&E findings, their use is limited by low staff capacity. The primary audience for the results remains the donor agency, and the primary motivation for M&E remains donor reporting. Reporting remains a burdensome affair, with ongoing limitations around streamlining results for donors. To reduce the burden of reporting for individual projects, the participants in our study suggested placing greater emphasis on process evaluations rather than impact evaluations. Participants also suggested increased data sharing between organizations working in the same regions and making better use of secondary data sources; in both cases to reduce the need for primary data collection. Conclusion We carried out this work to advance the conversation on how NGOs currently manage their M&E – a conversation which should involve NGOs, donors, local health system actors, and the communities with whom they work. More flexibility from donors, increased use of technology, and more transparency on if and how data is being used would help NGOs with their M&E process.
The Impact of Resilience, Health Literacy, and Social Support on Medication Adherence and Self-care Among Adults With Heart Failure

Background Personal and psychological factors, such as depression, have a considerable influence on nonadherence to medications and self-care in those with heart failure. More evidence is needed about positive personal factors that motivate adherence to medications and self-care in those with heart failure. Objective The purpose of this study was to investigate whether there was a relationship between the personal resources of resilience, hope, health literacy, social support, and self-care activation and adherence to HF self-care and medications and whether race impacts adherence. Methods This study used a cross-sectional, correlational design. Stepwise regression was used to test whether resilience, hope, health literacy, self-care activation, and race significantly predicted medication adherence and self-care. A diverse sample was recruited for this study. Results Of the 174 participants, 51% were female, 51.7% were White, and the mean age was 62 years. After adjustment for differences in age and depressive symptoms, a predictive relationship remained between resilience, health literacy, and medication adherence. Hope, activation, and race were not selected in the final regression model. A high level of perceived social support was the only predictor of better HF self-care. Conclusion Persons with heart failure may have better medication adherence and overall self-care if sufficiently resilient, health literate, and supported regardless of their degree of hope or activation. Race and age may be important factors to consider. More research is needed to understand the connection between resilience and medication adherence.
Hyperdontia in the Paraguayan Martha's marked gecko (Homonota marthae: Phyllodactylidae: Squamata)

Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA Milwaukee Public Museum, Milwaukee, Wisconsin, USA Bell Museum of Natural History, University of Minnesota, St Paul, Minnesota, USA Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, Villanova, Pennsylvania, USA
Preoperative testosterone and follicle stimulating hormone levels are important predictors for sperm retrieval by microdissection testicular sperm extraction in non‐mosaic Klinefelter syndrome

This study aimed to assess outcomes of microdissection testicular sperm extraction (MD‐TESE) and identify predictors for sperm retrieval (SR) in patients with non‐mosaic Klinefelter syndrome (NM‐KFS). We retrospectively evaluated 37 patients with NM‐KFS who underwent MD‐TESE. Data of age at operation, body mass index (BMI), testicular volume, serum luteinizing hormone (LH), follicle stimulating hormone (FSH), preoperative and postoperative testosterone levels with reduction ratio between the two values, and FSH/preoperative testosterone ratio were analysed. These patients were divided into two groups according to success or failure of SR: the successful and failure groups. Factors related to SR were evaluated by statistical analyses using the Mann–Whitney U test and logistic regression modelling. Regarding these factors, the cut‐off level was specified using the receiver operating characteristics (ROC) curve. Moreover, the percentage of SR at that level was assessed. A simple scoring model was developed based on the multivariate analysis. Fourteen patients underwent successful SR, whereas 23 experienced failure SR. Statistical analysis found preoperative testosterone and FSH levels to be significant factors associated with SR. On the ROC curve, the cut‐off levels for preoperative testosterone and FSH were 2.34 ng/ml and 33.2 mIU/ml respectively. A new scoring model was developed, consisting of preoperative testosterone (≥2.34 ng/ml) and FSH (≤33.2 mIU/ml). The sperm retrieval rates (SRRs) were clearly discriminated by stratification according to the scoring model. The SRR of the cases of scores of 2, 1 and 0 were 87.5%, 31.6% and 10% respectively. At our hospital, the SRR of MD‐TESE in patients with NM‐KFS was 37.8%. The patients with high testosterone and low FSH levels tended to demonstrate successful SR.
The safety and performance of the Spectra Optia apheresis system platelet depletion protocol in patients with elevated platelet counts

Thrombocytosis is a presenting and progressive clinical feature found in multiple disease states. It is characterized by high platelet (PLT) counts (>450 × 109/L) and can lead to thrombohemorrhagic events. Thrombocytapheresis or platelet depletion (PLTD) can be performed in acutely symptomatic patients suffering from thrombocytosis and may reduce or prevent acute serious complications associated with thrombocythemia thereby enabling patients to receive potentially curative high‐dose chemotherapy.