Miracle-dz/UniFAR-FTUs huggingface dataset:
A many-body model to study proteins. II. Incidence of many-body polarization effects on the interaction of the calmodulin protein with four Ca2+ dications and with a target enzyme peptide

The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one, and a better description of the Ca2+ binding sites (as compared to “small molecule” structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca2+ interactions. This is due to the inability of pairwise force fields to account for the strong anticooperative effects predicted to occur in [Ca,(carboxylate)n]2−n systems by both the many-body model and quantum computations. Hence, the new many-body model appears to be well suited for describing proteinic systems interacting with cations, both in terms of geometry and energy.The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one, and a better description of the Ca2+ binding sites (as compared to “small molecule” structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca2+ interactions. This is du.
Brief Research Report: Sense of Belonging and Academic Help-Seeking as Self-Regulated Learning

Abstract Academic help-seeking is a self-regulatory strategy that can have an important influence on students’ learning and achievement. The primary goal of the present study was to investigate whether college students’ sense of belonging could be used to understand their academic help-seeking. In addition, two aspects of motivation, self-efficacy for self-regulated learning and utility value, were examined as predictors of adaptive and expedient help-seeking strategies within an integrative model. College students (N = 307) completed two online self-report surveys that assessed sense of belonging, motivation, and help-seeking. Results of structural equation modeling showed that sense of belonging significantly predicted reported use of adaptive help-seeking strategies, even when accounting for students’ motivation. Self-efficacy for self-regulated learning also positively predicted adaptive help-seeking strategies, whereas utility value negatively predicted expedient help-seeking strategies. Findings support the conclusion that college students’ perceptions of their social contexts inform if and how they seek help with their learning.
Estimating and mitigating the effects of systemic low frequency oscillations (sLFO) on resting state networks in awake non-human primates using time lag dependent methodology

Aim Resting-state fMRI (rs-fMRI) is often used to infer regional brain interactions from the degree of temporal correlation between spontaneous low-frequency fluctuations, thought to reflect local changes in the BOLD signal due to neuronal activity. One complication in the analysis and interpretation of rs-fMRI data is the existence of non-neuronal low frequency physiological noise (systemic low frequency oscillations; sLFOs) which occurs within the same low frequency band as the signal used to compute functional connectivity. Here, we demonstrate the use of a time lag mapping technique to estimate and mitigate the effects of the sLFO signal on resting state functional connectivity of awake squirrel monkeys. Methods Twelve squirrel monkeys (6 male/6 female) were acclimated to awake scanning procedures; whole-brain fMRI images were acquired with a 9.4 Tesla scanner. Rs-fMRI data was preprocessed using an in-house pipeline and sLFOs were detected using a seed regressor generated by averaging BOLD signal across all voxels in the brain, which was then refined recursively within a time window of −16–12 s. The refined regressor was then used to estimate the voxel-wise sLFOs; these regressors were subsequently included in the general linear model to remove these moving hemodynamic components from the rs-fMRI data using general linear model filtering. Group level independent component analysis (ICA) with dual regression was used to detect resting-state networks and compare networks before and after sLFO denoising. Results Results show sLFOs constitute ~64% of the low frequency fMRI signal in squirrel monkey gray matter; they arrive earlier in regions in proximity to the middle cerebral arteries (e.g., somatosensory cortex) and later in regions close to draining vessels (e.g., cerebellum). Dual regression results showed that the physiological noise was significantly reduced after removing sLFOs and the extent of reduction was determined by the brain region contained in the resting-state network. Conclusion These results highlight the need to estimate and remove sLFOs from fMRI data before further analysis.
Angular photogrammetric soft tissue facial profile analysis of Bangladeshi young adults

Introduction: Angular photogrammetric soft tissue facial profile analysis provides a permanent record for the actual appearance of a person, which would also serve to establish an ideal esthetic treatment goal. The aim of the present study was to evaluate the average angular variables that define the soft tissue facial profile of a Bangladeshi sample. Materials and Methods: This cross-sectional study was carried out at Department of Orthodontics and Dentofacial Orthopedics of Dhaka Dental College and Hospital, Bangladesh, from July to December 2015. Soft tissue facial profiles of 200 participants (100 males and 100 females) between 18 and 25 years of age, with a dental Class I occlusal relationship and harmonious soft tissue profile, were selected by convenience sampling among students, doctors, and patients of Dhaka Dental College. Standardized photographs of 200 samples were taken in the natural head position. The photographic records were analyzed with the software for Windows, Microsoft Visio 2007, Standard Edition. All data were analyzed through standard methods using Statistical Package for the Statistical Package for Social Science Software (SPSS Version-20, IBM Corp, USA). Results: The average angular measurements for nasofrontal, total facial angle, facial angle, upper lip angle, projection of lower lip to chin, and mentolabial angle were wider in females. The mean value for nose tip angle, nasolabial angle, nasomental angle, and projection of upper lip to chin angle was higher in males compared to females. Nasofrontal angle (G-N-Nd) (P = 0.000) and mentolabial angle (Li-Sm-Pg) (P = 0.001) showed statistically significant differences. The greatest variability was found for mentolabial angle. Conclusion: The study of angular photogrammetric soft tissue facial profile analysis of Bangladeshi young adults contributes to the establishment of standardized normal values for the population. This study provides data which can be used in treatment planning by specialists such as orthodontists, prosthodontists, plastic surgeons, and maxillofacial surgeons, who have the capability to change the soft tissue facial features.
FORECASTING SOLID MEDICAL WASTE DEMAND USING EXTRAPOLATIVE DAILY DATA SETS: A CASE STUDY OF A MEDICAL SOLID WASTE PROCESSING SERVICE PROVIDER IN INDONESIA

Due to a service provider for collecting and incinerating of solid medical waste failed to fulfill the requirements of the Indonesian Ministry of Environment regarding the difficulties to predict the amount of medical solid waste in the primary and secondary source. This research was to study the most optimal time series model of demand forecast for service provider for solid medical waste incineration. In this study, the use of extensive records from past data required due to the need intensive supervision to handle infection risk and over demand that may happen every day. The forecasting methods analyzed included: moving average, weighted moving average, exponential smoothing, and exponential smoothing with trend adjustment. The optimal forecasting model was measured using Mean Absolute Deviation (MAD), Mean Square Error (MSE), and Mean Absolute Percent Error (MAPE). The result showed that exponential smoothing which assumed stable fluctuation of the actual value (α = 0.10) is the most optimal forecast model based on the values of MAD and MAPE. Meanwhile, based on MSE showed that MA (n = 7) was the most optimal forecasting model. The difference in optimal forecasting measurement models guide discretion to choose the right forecasting model based on optimal forecasting model interpretation.
Implementation of Web-Based Virtual Laboratory Media in Learning

The integration of information and communication technology in learning through the application of virtual laboratory media can be an alternative solution to overcome the constraints of time, cost, and laboratory safety in biology labs. Virtual laboratories are very suitable to be applied to the mechanism of evolution because they involve the context of space and time, and can provide opportunities for students to learn independently and increase active student involvement in learning. These study aims are to determine the effect of the application of virtual laboratory media on the understanding of student concepts; knowing increasing students' understanding of the concept of evolutionary mechanisms, and knowing students' responses after learning with virtual laboratories. This type of research is a pre-experimental design (nondesign) with one group pretest-posttest design. The research subjects were 37 students. The media used as many as 8 web-based virtual laboratory programs (online) that can be freely accessed. Data collection techniques include tests (pretest and posttest) and questionnaires. The pretest and posttest values were analyzed by the T-test while the questionnaire data were analyzed descriptively. The application of web-based virtual laboratory media on the evolution mechanism material influences the understanding of student concepts (t arithmetic> t table then H0 is rejected and H1 is accepted) The application of these media increases students' understanding of the concept of evolutionary mechanisms. The mean value increased from pretest 23.65 to 56.08 at the posttest with an increase of 32.43. Student responses to the application of media in learning showed 91.89% of students felt helped in understanding the process of evolution while 100% of students felt helped in understanding the role of evolution in causing evolution.
AIM2 and Psoriasis

Psoriasis is a chronic inflammatory skin disease occurring worldwide, with multiple systemic complications, which seriously affect the quality of life and physical and mental health of patients. The pathogenesis of psoriasis is related to the environment, genetics, epigenetics, and dysregulation of immune cells such as T cells, dendritic cells (DCs), and nonimmune cells such as keratinocytes. Absent in melanoma 2 (AIM2), a susceptibility gene locus for psoriasis, has been strongly linked to the genetic and epigenetic aspects of psoriasis and increased in expression in psoriatic keratinocytes. AIM2 was found to be activated in an inflammasome-dependent way to release IL-1β and IL-18 to mediate inflammation, and to participate in immune regulation in psoriasis, or in an inflammasome-independent way by regulating the function of regulatory T(Treg) cells or programming cell death in keratinocytes as well as controlling the proliferative state of different cells. AIM2 may also play a role in the recurrence of psoriasis by trained immunity. In this review, we will elaborate on the characteristics of AIM2 and how AIM2 mediates the development of psoriasis.
Wireless Underground Communications in Sewer and Stormwater Overflow Monitoring: Radio Waves through Soil and Asphalt Medium

Storm drains and sanitary sewers are prone to backups and overflows due to extra amount wastewater entering the pipes. To prevent that, it is imperative to efficiently monitor the urban underground infrastructure. The combination of sensors system and wireless underground communication system can be used to realize urban underground IoT applications, e.g., storm water and wastewater overflow monitoring systems. The aim of this article is to establish a feasibility of the use of wireless underground communications techniques, and wave propagation through the subsurface soil and asphalt layers, in an underground pavement system for storm water and sewer overflow monitoring application. In this paper, the path loss analysis of wireless underground communications in urban underground IoT for wastewater monitoring has been presented. The dielectric properties of asphalt, sub-grade aggregates, and soil are considered in the path loss analysis for the path loss prediction in an underground sewer overflow and wastewater monitoring system design. It has been shown that underground transmitter was able to communicate through thick asphalt (10 cm) and soil layers (20 cm) for a long range of up to 4 km.
Impact of ankylosing spondylitis on stroke limited to specific subtypes: Evidence from Mendelian randomization study

Background The relationship between Ankylosing Spondylitis (AS) and the risk of stroke is complex. Therefore, we utilized Two-Sample Mendelian randomization to examine the probable causal link between these two features. Methods The genetic instruments linked to AS were chosen from a summary-level genetic data set from the FinnGen consortium in people of European ancestry (1462 cases and 164,682 controls). Stroke and its subtypes were selected as outcomes, and the MEGASTROKE consortium population was used to identify the genetic associations of AS on stroke (40,585 cases and 406,111 controls), ischemic stroke (IS) (34,217 cases and 406,111 controls), and its subtypes including large artery stroke (LAS) (4373 cases and 146,392 controls), small vessel stroke (SVS) (5386 cases and 192,662 controls), and cardioembolic stroke (CES) (7193 cases and 204,570 controls). Intracerebral hemorrhage (ICH) (1687 cases and 201,146 controls) data set from the FinnGen consortium was also used. To obtain the casual estimates, the inverse variant weighted (IVW) method was mainly used. By examining the heterogeneity and pleiotropy of particular single nucleotide polymorphisms (SNPs), the robustness of the results was also examined. Results There was no evidence found to prove the correlation between genetically predicted AS and stroke (odds ratio [OR] 1.014; 95% confidence interval [CI] 0.999-1.031; P = 0.063), ICH (OR 1.030; 95% CI 0.995-1.067; P = 0.090), and IS (OR 1.013; 95% CI 0. 998-1.030; P = 0.090). In terms of the different subtypes of IS, there was strong evidence of positive causal inferences on CES (OR 1.051; 95% CI 1.022-1.081; P = 0.001), and suggestive evidence of positive causal inferences on LAS (OR 1.042; 95% CI 1.003-1.082; P = 0.033), while it was not significant for SVS (OR 1.010; 95% CI 0.975-1.047; P = 0.563). Conclusion This study suggests that the possible causative impact of genetically predicted AS on stroke may be restricted to the CES and LAS subtypes.
Racial and Sex Differences in the Response to First-Line Antihypertensive Therapy

Objective: As compared to whites, the black population develops hypertension (HTN) at an earlier age, has a greater frequency and severity of HTN, and has poorer control of blood pressure (BP). Traditional practices and treatment efforts have had minor impact on these disparities, with over a 2-fold higher death rate currently for blacks as compared to whites. The University of Mississippi Medical Center (UMC) is located in the southeastern US and the Stroke Belt, which has higher rates of HTN and related diseases as compared to the rest of the country. Methods: We retrospectively analyzed the UMC's Research Data Warehouse, containing >30 million electronic health records from >900,000 patients to determine the initial BP response following the first prescribed antihypertensive drug. Results: There were 5,973 white (45% overall HTN prevalence) and 10,731 black (57% overall HTN prevalence) patients who met criteria for the study. After controlling for age, BMI, and drug dosage, black males were overall less likely to have controlled BP (defined as < 140/90 mmHg) and were associated with smaller falls in BP as compared to whites and black females. Blockers of the renin-angiotensin system (RAS) failed to significantly improve odds of HTN control vs. the untreated group in black patients. However, our data suggests that these drugs do provide significant benefit in blacks when combined with THZ, as compared to untreated and as compared to THZ alone. Conclusion: These data support the use of a single-pill formulation with ARB or ACE inhibitor with a thiazide in blacks for initial first-line HTN therapy and suggests that HTN treatment strategies should consider both race and gender. Our study gives a unique insight into initial antihypertensive responses in actual clinical practice and could have an impact in BP control efficiency in a state with prevalent socioeconomic and racial disparities.
The Role of Caregiver Burden in Quality of Life and Perception of Patients with Chronic Kidney Failure on Hemodialysis

Background: Acute kidney failure is a common complication in critically ill patients of intensive care units. Objectives: The objective of this study was to examine the role of caregiver burden on quality of life and perception of patients with kidney failure. Methods: This descriptive-analytical study followed a correlational design. The statistical population included 191 patients with chronic kidney failure in the age range of 30 to 50 years old, who underwent hemodialysis at hospitals of Zahedan within 6 months, during year 2014. Overall, 54 patients were selected using the convenience sampling method. The measurement tools were the caregiver burden inventory (Novak and Guest, 1989), the quality of life scale (Rand, 1995), and the experience and perception of suffering scale (Schulz et al., 2010). Results: The results were analyzed using Pearson correlation coefficient and regression analysis. The results of the current study indicated that caregiver burden was positively and significantly correlated with physical and mental dimensions of quality of life and it was significantly and negatively related to physical and mental dimensions of perception of suffering. In addition, the results of regression analysis revealed that caregiver burden predicted 0.05 of mental and physical quality of life, 0.07 of physical perception of suffering, and 0.05 of mental perception of suffering. Conclusions: Therefore, development of community-based services, such as short-term hospitalizations, psychological and vocational rehabilitations, and follow-up treatments at home, which are among the main requirements of caregivers, need to be taken into consideration in national mental health programs.
Analyzing Predictive Factors Associated with the Variable Rates of Prevalence of Post-Traumatic Stress Disorder among National Guard/Reserve Soldiers Compared to Active Duty Soldiers: A Pilot Study

Research Aim: The aim for this study was to better understand the higher post-deployment prevalence of PTSD among National Guard/Reserve Soldiers compared to Active Duty Soldiers by analyzing the possible predictive factors associated with the variable rates. Since September 11th, 2001, the United States Army has deployed a significantly larger percentage of National Guard and Reserve forces to combat zones in support of Operation Enduring Freedom and Operation Iraqi Freedom. The United States Office of Veterans Affairs has reported increased suicide rates and suicide risk for Post-traumatic Stress Disorder (PTSD) for Soldiers deployed in support of these conflicts in particular. Few studies have assessed the relationship between military component (Active Duty vs. Reserve Component) and PTSD prevalence and risk factors but many of the studies that exist have reported higher rates in Reserve Component Soldiers as compared to Active Duty Soldiers. This study identifies and discusses possible implications for these specific vulnerabilities. Research Methods: The Deployment Risk and Resilience Inventory were used to assess the service members’ trauma-related experiences. The Connor-Davidson Resilience Scale was used to assess resiliency as a pre-existent factor inherent to the individual. The Treatment Reactions Scale was used to assess stigma for PTSD treatment. Statistical analysis of variance was performed using Graphpad Prism 6 Software to find if there were any statistical differences between prevalence rates. Linear regression analysis was used to determine correlations between predictive factors and PTSD within each component. Trial Registration: Philadelphia College of Osteopathic Medicine Institutional Review Board Protocol #H15-034X (April 13, 2015).
Staining of activated ß2-integrins in combination with CD137 and CD154 for sensitive identification of functional antigen-specific CD4+ and CD8+ T cells

Common flow cytometry-based methods used for functional assessment of antigen-specific T cells rely on de novo expression of intracellular cytokines or cell surface activation induced markers. They come with some limitations such as complex experimental setting, loss of cell viability and often high unspecific background which impairs assay sensitivity. We have previously shown that staining of activated ß2-integrins either with multimers of their ligand ICAM-1 or with a monoclonal antibody can serve as a functional marker detectable on T cells after minutes (CD8+) or few hours (CD4+) of activation. Here, we present a simple method for detection of activated ß2-integrins in combination with established cell surface activation induced markers. We observed that activated ß2-integrins were still detectable after 14 hours of stimulation, allowing their detection together with CD137 and CD154. Combinatorial gating of cells expressing activated ß2-integrins and CD137 or CD154 reduced background in unstimulated samples, increasing the signal-to-noise ratio and allowing improved assessment of low-frequency T cell responses. Extracellular staining of these markers highly correlated with production of intracellular cytokines IL-2, TNF or IFNγ in CD4+ and CD8+ T cells. As an exemplary application, SARS-CoV-2 spike-specific T cell responses were assessed in individuals after COVID-19 vaccination. This method should be useful for epitope discovery projects and for the simultaneous monitoring of low-frequency antigen-specific CD4+ and CD8+ T cell responses in various physiological situations.