Miracle-dz/UniFAR-FTUs huggingface dataset:
Hessian chain bracketing

Second derivatives of mathematical models for real-world phenomena are fundamental ingredients of a wide range of numerical simulation methods including parameter sensitivity analysis, uncertainty quantification, nonlinear optimization and model calibration. The evaluation of such Hessians often dominates the overall computational effort. The combinatorial {\sc Hessian Accumulation} problem aiming to minimize the number of floating-point operations required for the computation of a Hessian turns out to be NP-complete. We propose a dynamic programming formulation for the solution of {\sc Hessian Accumulation} over a sub-search space. This approach yields improvements by factors of ten and higher over the state of the art based on second-order tangent and adjoint algorithmic differentiation.
How to GENERALize Across Many Software Projects? (with case studies on Predicting Defect and Project Health)

Despite decades of research, SE lacks widely accepted models (that offer precise quantitative predictions) about what factors most influence software quality. This paper provides a “good news” result that such general models can be generated using a new transfer learning framework called “GENERAL”. Given a tree of recursively clustered projects (using project meta-data), GENERAL promotes a model upwards if it performs best in the lower clusters (stopping when the promoted model performs worse than the models seen at a lower level). The number of models found by GENERAL is minimal: one for defect prediction (756 projects) and less than a dozen for project health (1628 projects). Hence, via GENERAL, it is possible to make conclusions that hold across hundreds of projects at a time. Further, the models produced in this manner offer predictions that perform as well or better than prior state-of-the-art. To the best of our knowledge, this is the largest demonstration of the generalizability of quantitative predictions of project quality yet reported in the SE literature.
Spot the Difference: Detection of Topological Changes via Geometric Alignment

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.
Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.
Strategies to Investigate Membrane Damage, Nucleoid Condensation, and RNase Activity of Bacterial Toxin–Antitoxin Systems

A large number of bacterial toxin–antitoxin (TA) systems have been identified so far and different experimental approaches have been explored to investigate their activity and regulation both in vivo and in vitro. Nonetheless, a common feature of these methods is represented by the difficulty in cell transformation, culturing, and stability of the transformants, due to the expression of highly toxic proteins. Recently, in dealing with the type I Lpt/RNAII and the type II YafQ/DinJ TA systems, we encountered several of these problems that urged us to optimize methodological strategies to study the phenotype of recombinant Escherichia coli host cells. In particular, we have found conditions to tightly repress toxin expression by combining the pET expression system with the E. coli C41(DE3) pLysS strain. To monitor the RNase activity of the YafQ toxin, we developed a fluorescence approach based on Thioflavin-T which fluoresces brightly when complexed with bacterial RNA. Fluorescence microscopy was also applied to reveal loss of membrane integrity associated with the activity of the type I toxin Lpt, by using DAPI and ethidium bromide to selectively stain cells with impaired membrane permeability. We further found that atomic force microscopy can readily be employed to characterize toxin-induced membrane damages.
The Impact of Chronotype on the Sleep and Training Responses of Elite Female Australian Footballers

The primary aims of the present study were to examine the impact of chronotype on sleep/wake behaviour, perceived exertion, and training load among professional footballers. Thirty-six elite female professional football player’s (mean ± SD: age, 25 ± 4 y; weight, 68 ± 7 kg) sleep and training behaviours were examined for 10 consecutive nights during a pre-season period using a self-report online player-management system and wrist activity monitors. All athletes completed the Morningness-Eveningness Questionnaire (rMEQ) on the first day of data collection. Eleven participants were morning types, seventeen participants were intermediate types, and three participants were evening types. Separate linear mixed models were conducted to assess differences in sleep, perceived exertion, and training behaviours between chronotype groups. Morning types woke up earlier (wake time: 07:19 ± 01:16 vs. 07:53 ± 01:01, p = 0.04) and reported higher ratings of perceived exertion compared to intermediate types (6.7 ± 1.1 vs. 5.9 ± 1.2, p = 0.01). No differences were observed between chronotype groups for bedtime, time in bed, total sleep time, sleep efficiency, training duration, or training load. In circumstances where professional female football players are required to train at a time opposing their natural circadian preference (e.g., morning type training in the evening), their perceived exertion during training may be higher than that of players that are training at a time that aligns with their natural circadian preference (e.g., evening type training in the evening). It is important for practitioners to monitor individual trends in training variables (e.g., rating of perceived exertion, training load) with relation to athlete chronotype and training time. Future research should examine the relationship between chronotype, training time, and rating of perceived exertion across different training durations.
Association between prehospital field to emergency department delta shock index and in-hospital mortality in patients with torso and extremity trauma: A multinational, observational study

Hemorrhage, a main cause of mortality in patients with trauma, affects vital signs such as blood pressure and heart rate. Shock index (SI), calculated as heart rate divided by systolic blood pressure, is widely used to estimate the shock status of patients with hemorrhage. The difference in SI between the emergency department and prehospital field can indirectly reflect urgency after trauma. We aimed to determine the association between delta SI (DSI) and in-hospital mortality in patients with torso or extremity trauma. Patients with DSI >0.1 are expected to be associated with high mortality. This retrospective, observational study used data from the Pan-Asian Trauma Outcomes Study. Patients aged 18–85 years with abdomen, chest, upper extremity, lower extremity, or external injury location were included. Patients from China, Indonesia, Japan, Philippines, Thailand, and Vietnam; those who were transferred from another facility; those who were transferred without the use of emergency medical service; those with prehospital cardiac arrest; those with unknown exposure and outcomes were excluded. The exposure and primary outcome were DSI and in-hospital mortality, respectively. The secondary and tertiary outcome was intensive care unit (ICU) admission and massive transfusion, respectively. Multivariate logistic regression analysis was performed to test the association between DSI and outcome. In total, 21,534 patients were enrolled according to the inclusion and exclusion criteria. There were 3,033 patients with DSI >0.1. The in-hospital mortality rate in the DSI >0.1 and ≤0.1 groups was 2.0% and 0.8%, respectively. In multivariate logistic regression analysis, the DSI ≤0.1 group was considered the reference group. The unadjusted and adjusted odds ratios of in-hospital mortality in the DSI >0.1 group were 2.54 (95% confidence interval [CI] 1.88–3.42) and 2.82 (95% CI 2.08–3.84), respectively. The urgency of traumatic hemorrhage can be determined using DSI, which can help hospital staff to provide proper trauma management, such as early trauma surgery or embolization.
Student Pharmacists during the Pandemic: Development of a COVID-19 Knowledge, Attitudes, and Practices (COVKAP) Survey

Background: The COVID-19 pandemic has caused innumerable changes to all aspects of human life and behavior, including academic life. This study describes the development of a COVID-19 Knowledge, Attitudes, and Practices (COVKAP) Survey among U.S. student pharmacists. The survey was administered at Doctor of Pharmacy programs in three states—Tennessee, Ohio, and Pennsylvania. Methods: The COVKAP survey—an online cross-sectional survey—was distributed to U.S. student pharmacists enrolled in three different colleges of pharmacy in three states during the fall semester of 2020. The survey was developed using literature review and Dillman’s recommendations for survey design. The COVKAP survey consisted of 23 closed and Likert-scale questions, and three open-ended questions. The research team conducted descriptive and inductive thematic analyses on the quantitative and qualitative data, respectively using SPSS (v27) and Dedoose® software. Results: A total of 421 responses were received. Respondents were predominantly female (72%) and White (79%). The average age of respondents was 23.4 years. The qualitative analysis revealed three themes: (1) Wellbeing and mental health struggles; (2) Being part of the decision-making process; (3) Necessity of adequate protection measures. Conclusions: Preliminary study findings indicate that student pharmacists’ concerns and the challenges that they face in their academic pursuits are largely similar across the three states in this study and inform about the importance of recognizing and mitigating the impact of widespread disruption in education. This disruption provides an opportunity for pharmacy academia to examine practices and methods that can be improved upon to help students become successful practitioners.
Investigation of external quality factor and coupling coefficient for a novel SIR based microstrip tri-band bandpass filter

In this article, a new method is developed to design a three-band miniaturized bandpass filter (BPF) that uses two asymmetrically coupled resonators with one step discontinuity and open-circuited uniform impedance resonator (UIR) to achieve Global Interoperability with Microwave Access (WiMAX) and Radio Frequency Identification (RFID) applications. First, a pair of asymmetrical step impedance resonators (ASIR) is used to implement a dual band filter, then a half wavelength uniform impedance resonator is added below to the transmission line to achieve a triple band response. The proposed filter resonates at frequencies of 3.7 GHz, 6.6 GHz, and 9 GHz with the fractional bandwidth of 7.52%, 5.1%, and 4.44%, respectively. By adjusting the physical length ratio (α) and the impedance ratio (R) of the asymmetric SIR, the proposed fundamental frequencies of the triple BPF are obtained. Moreover, the coupling coefficient (Ke) and external quality factor (Qe) are investigated between the resonators and the input/output ports of the transmission line and are calculated using full-wave EM simulator HFSS. In addition, five transmission zeros are introduced near the passbands to increase the filter selectivity. Finally, the proposed filter is designed and fabricated with a size of 13.69 × 25 mm (0.02 λg × 0.03 λg), where λg represents the guiding wavelength in the first passband. The simulated and measured results have a good correspondence, thus confirming the design concept.
Staphylococcus aureus derived hyaluronic acid and bacillus Calmette-Guérin purified proteins as immune enhancers to rabies vaccine and related immuno-histopathological alterations

Purpose One of the essential goals regarding the successful control of rabies infection is the development of a safe, effective, and inexpensive vaccine. the current study aimed to evaluate the inactivation potential of β-propiolactone (βPL), binary ethyleneimine (BEI), and hydrogen peroxide (H2O2). Materials and Methods Estimating the inactivation kinetics of βPL, BEI, and H2O2 revealed that the tested inactivants could completely and irreversibly inactivate rabies virus within 2, 12, and 4 hours, respectively while maintaining its viral immunogenicity. The potency of βPL, BEI, and H2O2 inactivated vaccines was higher than the World Health Organization acceptance limit and were in the order of 3.75, 4.21, and 3.64 IU/mL, respectively. Monitoring the humoral and cellular immunity elicited post-immunization using Staphylococcus aureus derived hyaluronic acid (HA) and bacillus Calmette-Guérin purified protein derivative (PPD) adjuvanted rabies vaccine candidates were carried out using enzyme-linked immunosorbent assay. Results Results demonstrated that both adjuvants could progressively enhance the release of anti-rabies total immunoglobulin G as well as the pro-inflammatory mediators (interferon-gamma and interleukin-5) relative to time. However, a higher immune response was developed in the case of HA adjuvanted rabies vaccine compared to PPD adjuvanted one. The harmful consequences of the tested adjuvants were considered via investigating the histopathological changes in the tissues of the immunized rats using hematoxylin and eosin stain. Lower adverse effects were observed post-vaccination with HA and PPD adjuvanted vaccines compared to that detected following administration of the currently used alum as standard adjuvant. Conclusion Our findings suggested that HA and PPD could serve as a promising platform for the development of newly adjuvanted rabies vaccines with elevated immune enhancing potentials and lower risk of health hazards.
Application of “Magnetic Anchors” to Align Collagen Fibres for Axonal Guidance

The use of neural scaffolds with a highly defined microarchitecture, fabricated with standard techniques such as electrospinning and microfluidic spinning, requires surgery for their application to the site of injury. To circumvent the risk associated with aciurgy, new strategies for treatment are sought. This has led to an increase in the quantity of research into injectable hydrogels in recent years. However, little research has been conducted into controlling the building blocks within these injectable hydrogels to produce similar scaffolds with a highly defined microarchitecture. “Magnetic particle string” and biomimetic amphiphile self-assembly are some of the methods currently available to achieve this purpose. Here, we developed a “magnetic anchor” method to improve the orientation of collagen fibres within injectable 3D scaffolds. This procedure uses GMNP (gold magnetic nanoparticle) “anchors” capped with CMPs (collagen mimetic peptides) that “chain” them to collagen fibres. Through the application of a magnetic field during the gelling process, these collagen fibres are aligned accordingly. It was shown in this study that the application of CMP functionalised GMNPs in a magnetic field significantly improves the alignment of the collagen fibres, which, in turn, improves the orientation of PC12 neurites. The growth of these neurite extensions, which were shown to be significantly longer, was also improved. The PC12 cells grown in collagen scaffolds fabricated using the “magnetic anchor” method shows comparable cellular viability to that of the untreated collagen scaffolds. This capability of remote control of the alignment of fibres within injectable collagen scaffolds opens up new strategic avenues in the research for treating debilitating neural tissue pathologies.
Item Response Theory Investigation of Misophonia Auditory Triggers

Misophonia is characterised by a low tolerance for day-to-day sounds, causing intense negative affect. This study conducts an in-depth investigation of 35 misophonia triggers. A sample of 613 individuals who identify as experiencing misophonia and 202 individuals from the general population completed self-report measures. Using contemporary psychometric methods, we studied the triggers in terms of internal consistency, stability in time, precision, severity, discrimination ability, and information. Three dimensions of sensitivity were identified, namely, to eating sounds, to nose/throat sounds, and to general environmental sounds. The most informative and discriminative triggers belonged to the eating sounds. Participants identifying with having misophonia had also significantly increased odds to endorse eating sounds as auditory triggers than others. This study highlights the central role of eating sounds in this phenomenon and finds that different triggers are endorsed by those with more severe sound sensitivities than those with low sensitivity.
Staged Repair Using Modified Bishop-Koop Procedure in Complicated Congenital Colonic Atresia in a Neonate

Colonic atresia (CA) is the rarest type of intestinal atresia and is defined as an obstruction in the large intestinal lumen. This is a rare case presentation of a four-day-old full-term female patient presented with signs and symptoms of intestinal obstruction. Investigation revealed that she had complicated CA located in the splenic flexure. Laparotomy and colostomy were done on the patient. About two months later, she was admitted for stoma closure, which was converted to modified Bishop-Koop stoma. Lastly, the patient underwent a successful stoma closure. Upon one month of follow-up, the patient's condition has markedly improved and the wound healed well without any complications.
Prostate Magnetic Resonance Imaging Analyses, Clinical Parameters, and Preoperative Nomograms in the Prediction of Extraprostatic Extension

Introduction: Proper planning of laparoscopic radical prostatectomy (RP) in patients with prostate cancer (PCa) is crucial to achieving good oncological results with the possibility of preserving potency and continence. Aim: The aim of this study was to identify the radiological and clinical parameters that can predict the risk of extraprostatic extension (EPE) for a specific site of the prostate. Predictive models and multiparametric magnetic resonance imaging (mpMRI) data from patients qualified for RP were compared. Material and methods: The study included 61 patients who underwent laparoscopic RP. mpMRI preceded transrectal systematic and cognitive fusion biopsy. Martini, Memorial Sloan-Kettering Cancer Center (MSKCC), and Partin Tables nomograms were used to assess the risk of EPE. The area under the curve (AUC) was calculated for the models and compared. Univariate and multivariate logistic regression analyses were used to determine the combination of variables that best predicted EPE risk based on final histopathology. Results: The combination of mpMRI indicating or suspecting EPE (odds ratio (OR) = 7.49 (2.31–24.27), p < 0.001) and PSA ≥ 20 ng/mL (OR = 12.06 (1.1–132.15), p = 0.04) best predicted the risk of EPE for a specific side of the prostate. For the prediction of ipsilateral EPE risk, the AUC for Martini’s nomogram vs. mpMRI was 0.73 (p < 0.001) vs. 0.63 (p = 0.005), respectively (p = 0.131). The assessment of a non-specific site of EPE by MSKCC vs. Partin Tables showed AUC values of 0.71 (p = 0.007) vs. 0.63 (p = 0.074), respectively (p = 0.211). Conclusions: The combined use of mpMRI, the results of the systematic and targeted biopsy, and prostate-specific antigen baseline can effectively predict ipsilateral EPE (pT3 stage).
Oral immunization of rat with chromosomal expression LipL32 in attenuated Salmonella vaccine induces immune respond against pathogenic Leptospira

Purpose Leptospirosis caused by Leptospira spp. remains a global health problem. Available commercial leptospiral vaccines have shown an ineffective prevention for leptospiral infection. The aim of this study was to develop leptospirosis vaccine using recombinant attenuated Salmonella vaccine (RASV) as a platform. We expected that this vaccine has ability to continuous and strongly stimulate immune systems including protective mucosal, humoral, and cell mediated immunity in rat model. Materials and Methods In this study, we engineered RASV, NRSL32 strain containing chromosomal fusion between nucleotides encoding secretion signal of SPI-2 effector protein, SspH2 and gene encoding major pathogenic leptospiral outer membrane lipoprotein, LipL32. Subsequently, our modified RASV was oral vaccination to rat and blood samples were taken for assessment of immune responses. Results Our Salmonella NRSL32 strain showed expression and secretion of SspH21-215-LipL32 recombinant protein via SPI-2 T3SS. After oral administration of NRSL32 strain to rats, significant titers of total immunoglobulin G (IgG) and immunoglobulin A against rLipL32 were observed in long period up to 77 days after vaccination. The stimulated antibody showed ability to specific bind with LipL32 protein on surface of pathogenic Leptospira spp. Additionally, the balance level of IgG2a/IgG1 ratio and level of interferon-γ and interleukin-4 secretion were detected. Conclusion The results showed that our RASV platform with chromosomal expression elicited effective immune responses to leptospiral antigen. Moreover, this platform was capable for simultaneous stimulation of Th1 and Th2-biased responses. Further investigation is necessary study of protective efficacy against leptospiral infection in animal models.