Miracle-dz/UniFAR-FTUs huggingface dataset:
The unified Monte Carlo model of photon migration in scattering tissue-like media for the needs of Biomedical Optics

Nowadays optical and laser-based diagnostics technologies are widely used in many fields such as oncology, vascular and developmental biology, dermatology, pharmacy, materials sciences, food, and the cosmetic and health care industries. Optical techniques have a number of advantages over traditional methods and provide a broad variety of practical solutions for non-invasive diagnostics in a range of studies from single cells to biopsy of specific biological tissues and even whole organs. Conceptual design of a particular optical diagnostics system for non-invasive in vivo measurements of structural alterations in biological tissues and changes in their physiological properties requires careful selection of various technical parameters, including wavelength, coherence, polarization and intensity profile of incident optical radiation, sensitivity of the detector, size, and the geometry and mutual position of source and detector. When applied to biological tissues, multiple scattering of light overwhelmingly prevents laser-based techniques from providing high quality images of tissue structure and structural changes. Thus, comprehensive studies of optical radiation propagation and signal formation are required. Due to the complex inhomogeneous structure of biological tissues no general analytical solution exists that can describe the detected optical signal and how it is affected by structural or physiological changes. However, there is an exceptional example of a stochastic approach: the Monte Carlo method. Without extrinsic or intrinsic constraints, throughout the years the Monte Carlo method has been a gold standard for the assessment of optical radiation propagation and spacial localization of signals in biological tissues. Nonetheless, previously developed Monte Carlo models were extremely resource consuming and suffered from serious disadvantages, considerably limiting their applications. Due to the diversity of existing optical diagnostics modalities the development of a new Monte Carlo code was typically required for a particular practical application. This thesis describes the work that has gone into the development of the unified Monte Carlo model and considers its applications for the particular needs of biomedical optics. By utilizing the developed model, an intimate investigation of optical radiation propagation in highly scattering randomly inhomogeneous media such as biological tissues has been carried out. Further developments of the method and a complete theoretical background are presented. Emphasis is given to including the method the coherent properties of optical radiation. The developed model supports of a variety of configurations corresponding to the actual experimental conditions. The code of the developed model has been generalized and unified for multi-purpose use for various applications in biomedical optics utilizing object oriented programming. A dramatic speed up of simulations has been achieved A DO RO NI N
Frequent apocrine changes in pleomorphic adenoma with malignant transformation: a possible pre-malignant step in ductal carcinoma ex pleomorphic adenoma

Background The most common type of carcinoma ex pleomorphic adenoma (CPA) is histologically equivalent to salivary duct carcinoma, which has an apocrine phenotype. Invasive CPA is often accompanied by non-invasive or in situ carcinoma, an observation that suggests the presence of precursor lesions. The aim of this study was to identify candidate precursor lesions of CPA within pleomorphic adenoma (PA). Methods Eleven resected cases of CPA with residual PA and 17 cases of PA with atypical changes were subjected to immunohistochemistry (IHC) for p53, human epidermal growth factor receptor 2 (HER2), androgen receptor (AR), pleomorphic adenoma gene 1, gross cystic disease fluid protein-15 (GCDFP-15), and anti-mitochondrial antibody. Results Invasive or in situ carcinoma cells in all CPAs were positive for AR, GCDFP-15, and HER2. Atypical foci in PAs corresponded to either apocrine or oncocytic changes on the basis of their reactivity to AR, GCDFP-15, and anti-mitochondrial antibody. Atypical cells in PAs surrounding CPAs had an apocrine phenotype without HER2 expression. Conclusions Our study identified frequent apocrine changes in residual PAs in CPA cases, suggesting a possible precursor role of apocrine changes. We recommend the use of HER2 IHC in atypical PAs, and that clinicians take HER2 positivity into serious consideration.
Pathways to Offense Charging: Examining Defense Decision-Making During Case Processing

Prosecutors are afforded significant discretionary power in the current justice system. While much attention has been given to the factors that influence charging decisions, little is known about decision-making in the charging process itself. Moreover, research has yet to examine the mechanisms used to initiate charging: grand jury indictments or the information. As these charging processes are characteristically different and may have significant implications for case processing and justice outcomes, it is important to explore what factors influence decision-making at this early stage. The current study addresses these shortcomings using case-processing data from a large urban jurisdiction. Results indicate significant differences between defendants charged via grand jury and information processes. In addition, charging pathways have important consequences for case outcomes.
Endothelial progenitor cells and major adverse cardiovascular events in patients receiving elective coronary angiography

Background and purpose: The association of circulating endothelial progenitor cells (EPCs) with different cardiovascular diseases and their related major adverse cardiovascular events (MACE) remained inconclusive. We aimed to clarify associations between the circulating EPC levels and the risk of MACE concerning different atherosclerosis-related diseases. Methods: This prospective cohort study was conducted from December 2009 to March 2015. Patients who underwent non-emergent coronary angiography (CAG) were included. The circulating EPC levels were measured using flow cytometry prior to the CAG procedure. The study evaluation of circulating EPC levels among patients with obstructive coronary artery disease (CAD) and other comorbidities. Patients were then assigned to tertiles by circulating EPC levels to evaluate the predictive values of the development of MACEs. Results: The study enrolled 1099 patients, of whom, 736 (67%) were men, with a mean age of 66.7 ± 12.5 years old. Overall, 637 (58%) patients were diagnosed with obstructive CAD according to CAG. MACE occurred in 268 (24.4%) patients. Circulating EPC levels were lower in patients with peripheral artery disease (PAD) but not associated with the presence of obstructive CAD, atrial fibrillation, chronic kidney disease (CKD), heart failure, and diabetes mellitus. Higher circulating EPC levels are linked with higher MACE among patients with suspected CAD, regardless of the presence or absence of obstructive CAD or CKD. The association did not present in patients with PAD. Conclusions: Higher circulating EPC levels are associated with a greater risk of MACE, regardless of the presence of obstructive CAD or CKD. This association was not apparent in the patients with PAD, suggesting impaired endothelial repair in these patients.
Green HRM and Sustainable Performance in Malaysian Hotels

Due to the business complexity and competitive environment, hotels are paying great attention to improve their sustainability performance through greening their workforce. Thus, this study examines the role of Green HRM practices in attaining sustainable environmental performance in Malaysian hotels while considering the crucial role of employees' pro-environmental attitudes, green behaviors, and green work climate perceptions. Data were collected from the employees who were directly engaged in implementing green practices in selected hotels. A survey questionnaire was used for data collection, and about 350 responses were received and applied for analysis through PLS-SEM. Findings revealed that Green HRM practices (green training and involvement, green performance management and compensation) positively and significantly influence employees' pro-environmental attitudes, further promoting green behaviors. It was also found that employees' green behaviors are the key contributors to spurring sustainable hotel performance. Therefore, this study might support decision-makers in understanding the role of Green HR practices in greening the workforce in the hospitality industry context.
Does Better Post-Thaw Motility of Dog Sperm Frozen with CLC Mean Better Zona Pellucida Binding Ability?

Simple Summary New cryopreservation methods for dog semen are constantly under investigation because the fertility results after insemination with frozen–thawed semen are still not satisfying. Most researchers do not investigate the fertilization ability of spermatozoa after the modification of cryopreservation protocols. In this study, we investigated whether spermatozoa membrane fluidity modification by use of cholesterol-loaded cyclodextrins (CLC) can improve kinematic parameters and also this method’s effects on capacitation status and fertilization ability. The lowest concentration of CLC increased motility parameters and percentage of live spermatozoa without cholesterol efflux compared to the control. There was no change in capacitation status but the binding ability of the sperm to the oocyte was decreased. Overall, these data suggest that improvement of kinematic parameters does not necessarily improve the zona pellucida binding ability results of canine spermatozoa. Abstract Even though the search for methods improving cryopreservation of canine spermatozoa led to an improvement of post-thaw quality, fertilizing results after insemination with frozen–thawed semen are still not satisfying. In this study, we focused on modification of spermatozoa membrane fluidity and investigated whether kinematic parameters as assessed by computer-assisted semen analyzer (CASA) can be improved. The primary aim of our study was to investigate whether the use of cholesterol-loaded cyclodextrins (CLC; 0.5 mg, 1 mg, 2 mg) and 2-Hydroxypropyl-ß-cyclodextrin (HBCD; 1 mg) positively influence capacitation status as examined by tyrosinphosphorylation, cholesterol efflux and zona binding assay (ZBA) of spermatozoa. The use of 0.5 mg of CLC increased the percentage of motile, progressive and rapid spermatozoa compared to the control. Addition of HBCD decreased motility and progressive motility of spermatozoa and the population with rapid movement in comparison to the control. The percentage of live spermatozoa without efflux of cholesterol compared to the control was increased when extender with 0.5 mg of CLC was used. There was no change in capacitation status. The zona binding ability of spermatozoa was significantly lower in the group with 0.5 mg of CLC than in the control. In conclusion, these results suggest that improvement of kinematic parameters does not necessarily coincide with better zona pellucida binding ability of spermatozoa.
A realizable force feedback-feedforward control loop for a piston wave absorber

We consider the problem of the absorption of 2D water waves by the horizontal motions of a vertical plane in response to the hydrodynamical force it experiences. The solution of this problem is straightforward in the frequency domain. Unfortunately, the transposition of the frequency domain solution to the time domain by inverse Fourier transforming leads to a non-causal impulse response function. Thus it cannot be used just as it is, neither as a control loop for physical absorbing devices nor as a non radiating boundary condition (NRBC) in numerical modeling. In this paper, we propose a method to derive causal approximations of this ideal controller. Two time-domain absorbing relations are proposed, differing in whether or not one knows a dominant frequency of the incident wave train to be absorbed. Their performances are compared with the absorption efficiency of the low frequency asymptotic Sommerfeld relation which simply reads, for such a piston device: U(t)=F(t).
Prevalence and Associated Factors of Ocular Manifestations of Acquired Immune Deficiency Syndrome Among Adults at University of Gondar Hospital, North West Ethiopia, 2021

Introduction Acquired immune deficiency syndrome is a disease with common clinical ocular manifestations. Ocular manifestations lead to blindness, which has a common social and economic impact. Purpose This study aimed to assess the prevalence and associated factors of ocular manifestations of acquired immune deficiency syndrome among adults at the University of Gondar Hospital, North West Ethiopia, 2021. Patients and Methods A cross-sectional study was conducted on 401 patients from June to August 2021. Samples were selected based on a systematic random sampling technique. Data collection was done using structured questionnaires. Data extraction format was used to collect the clinical characteristics of patients including ocular manifestations. Data entry was done by EpiData version 4.6. 0.6 and exported to the Statistical Package for the Social Sciences version 26 for data analysis. Associated factors were analyzed by binary logistic regression. P-value <0.05 with a 95% confidence level was used to declare a significant association. Results A total of 401 patients were involved with a response rate of 91.5%. The overall prevalence of ocular manifestations of acquired immune deficiency syndrome was 28.9%. The common ocular manifestations were seborrheic blepharitis at 16.4% and squamoid conjunctival growth at 4.5%. Age >35 years (AOR=2.52, 95% CI: 1.19, 5.35), Clusters of differentiation 4 count <200 cells/µL (AOR=4.76, 95% CI:2.50, 9.09), World Health Organization stage II (AOR=2.60, 95% CI: 1.23, 5.50), history of eye disease (AOR=3.05, 95% CI: 1.38, 6.72), and duration of Human Immunodeficiency Virus >5 years (AOR=2.79, 95% CI: 1.29, 6.05) were statistically associated with the ocular manifestation of acquired immune deficiency syndrome. Conclusion and recommendations In this study, the prevalence of ocular manifestation of acquired immune deficiency syndrome was high. Age, CD4 count, duration of HIV, eye disease history, and WHO clinical staging were the significant factors. Early eye checkups and regular ocular examinations of HIV patients would be helpful.
Researcher Perceptions of Involving Consumers in Health Research in Australia: A Qualitative Study

There is growing recognition internationally of the importance of involving consumers, patients, and the public in research. This is being driven by political mandates for policies, funding, and governance that demand genuine and meaningful engagement with consumers. There are many potential benefits to involving consumers in research, including an increased relevance to patient needs, improved quality and outcomes, and enhanced public confidence in research. However, the current literature highlights that efforts to incorporate their contributions are often tokenistic and there is a limited understanding of the psychological factors that can impact researcher attitudes, intentions, and behaviours when working with consumers in research. To address this gap, this study conducted 25 semi-structured interviews with health researchers in Australia using the qualitative case study method. The study aim was to explore the underlying influences on researcher behaviour when involving consumers in health research. The results identified several factors that influence researchers’ behaviour, including better quality research, emotional connection and the humanisation of research, and a shift in research culture and expectations as major drivers. However, beliefs that consumers would hinder research and must be protected from risks, paternalism, and a lack of researcher skills and resources were identified as major barriers. This article presents a theory of planned behaviour for consumer involvement in the health research model. The model offers a valuable tool for policymakers and practitioners to understand the factors that influence researcher behaviours. It can also serve as a framework for future research in this area.
A New Approach to Radiative Transfer in Galaxies

In this thesis, we present a novel algorithm for computing the radiation field in astrophysical simulations. The algorithm is tree-based, similar to many gravity solvers, and allows computation of radiative transfer in O(Nsink logNsource) in cases without absorption, and O(Nsink logNsource logN) time with absorption. The algorithm scales well with the number of processors due to its tree-based nature, and is highly tunable in accuracy and speed. It is also only weakly dependent on both the energy band and the number of energy bands used. We provide a suite of tests of the code showing its ability to create accurate fluxes, ionization fronts, hydrodynamics coupling, and shadowing. We apply the algorithm in a set of simulations on an isolated spiral galaxy from the AGORA project. The algorithm is used to calculate FUV fields within the galaxy, which self-consistently sets the dominant photoelectric heating in the gas. This has never before been performed in galaxy simulations. We find, in agreement with Ostriker et al. [2010], that FUV can be a very important regulation mechanism for star formation in a galaxy. Depending on the assumed opacity, FUV can decrease the average star formation rate (SFR) anywhere from 15% to a factor of twenty. We compare this regulation mechanism to a highly effective model of supernovae (SNe) feedback, which reduces the SFR by a factor of twenty as well. However, SNe feedback destroys most of the gas structure in the process, whereas FUV has minimal impact on the gas structure. In the simulations with FUV radiation, we are also able to create a two phase medium that is a function of the mean FUV intensity the gas receives. Finally, we find that simulations with FUV agree well with observations of nearby spirals on the Kennicutt-Schmidt relation, at least at gas surface densities of 0.2 30 M⊙. At surface densities higher than 30 M⊙, we find that FUV is not an effective regulator which is consistent with arguments that SNe or other feedback mechanisms should become the primary regulator.
Effect of addition of some enzymes on the acceleration of Ras cheese manufactured with addition of Goat’s milk

T HE objective of the present study was to accelerate the ripening of the Egyptian hard cheese (Ras cheese) by addition of goat milk, lipase and protease enzyme.Ras cheese treatments were manufactured as follows, control (C) Ras cheese manufactured from 100% cow milk,T1: Ras cheese manufactured from 80% cow milk and 20% goat milk, T2: Ras cheese manufactured from 80% cow milk and 20% goat milk and treated with 0.005% protease enzyme, T3: Ras cheese manufactured from 80% cow milk and 20% goat milk and treated with 0.01% protease enzyme,T4: Ras cheese manufactured from 80% cow milk and 20% goat milk and treated with 0.02% lipase enzyme, T5: Ras cheese manufactured from 80% cow milk and 20% goat milk and treated with 0.04% lipase enzyme. Chemical, sensory and texture profile analysis of the cheese during 90 days of ripening period were evaluated. There was a significant increase in most chemical analysis and a significant decrease in moisture content between all treatments with ripening period progress. For sensory evaluation, total score values showed a significant increase between all treatments with ripening period progress, except for T5 (45 and 90 days) which showed anon significant decrease in total score values especially after 45 days from ripening period, when compared with T1 and T2 (fresh) and a significant decrease when compared with other treatments. The highest values were observed for total score values (T1 90 days), while the lowest values were observed for (T4 fresh) when compared with other treatments.
Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies

Simple Summary SMARCA4-mutated tumors are associated with poor prognosis. However, it is not clear if male and female patients have the same or different prognosis and if additional common mutations within the tumor play a role in prognosis. We have found that male patients had substantially worse prognosis than female patients whose tumor carried a SMARCA4 mutation. In addition, different co-existing mutations including the mutation of TP53, KRAS, CDKN2A, STK11, and Keap1 were associated with differential prognosis. Our study provides helpful insight for prognostic stratification in clinical practice and for understanding the pathogenic mechanism of this unique subtype of malignancy. Abstract Background: Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. Methods: This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. Results: Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92–3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76–73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04–4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87–7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06–1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12–22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16–148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89–26.61}) were associated with worse OS. Conclusion: In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.