Miracle-dz/UniFAR-FTUs huggingface dataset:
Continuous Non-Invasive Arterial Pressure Monitoring (ClearSight System) and Ankle Blood Pressure Measurements as Alternatives to Conventional Arm Blood Pressure

Measuring blood pressure (BP) via a pneumatic cuff placed around the arm has long been the standard method. However, in clinical situations where BP monitoring at the arm is difficult, the ankle is frequently used instead. We compared continuous non-invasive blood pressure (CNBP) measurements obtained at the finger, ankle BP and arm BP in patients undergoing breast cancer surgery. Arm BP, ankle BP (both obtained with a conventional pneumatic cuff) and CNBP measurements were obtained every 2.5 min during surgery. Correlation and Bland–Altman analyses were performed and differences among measurements were analyzed using a linear mixed model. A total of 245 sets of BP measurements were obtained from 10 patients. All systolic blood pressure (SBP), diastolic blood pressure (DBP) and mean blood pressure (MBP) measurements of ankle BP and CNBP were positively correlated with the arm BP measurements (Spearman rho 0.688–0.836, p < 0.001 for each correlation). The difference between CNBP and arm SBP was significantly smaller (least squares mean (95% confidence interval): −6.03 (−11.40, −0.67)) compared to that between ankle and arm SBP (least squares mean (95% CI): −15.32 (−20.69, −9.96), p = 0.019). However, this significant difference was not observed in DBP and MBP (−1.23 vs. 1.75, p = 0.190 and −3.85 vs. −2.63, p = 0.604, respectively). Ankle SBP measurements showed larger differences from arm SBP measurements than did CNBP SBP measurements in patients undergoing breast cancer surgery. CNBP could serve as a useful alternative to ankle BP when standard arm BP measurements cannot be obtained.
Evaluation of bacterial culture and their resistant pattern in pus containing patients of different wards of the hospital, Lahore, Pakistan

In health care delivery worldwide, infections acquired in health care setting are the most challenging factors. Infections due to antibiotic resistant bacteria have increased day by day in both developed and developing countries. This study is performed to screen the bacterial pathogens present in pus samples taken from patients of different wards of hospital. Isolation of bacteria was determined by standard microbial techniques. Total number of samples is 383 in which 252 were males and 131 were females. 265 samples have growth (259 were suitable for culturing and other 6 were not suitable for culturing) and 118 samples have no growth. Most samples have single growth, while some samples have mixed growth. The predominant genera were coliform including Escherichia coli, Klebsiella, Pseudomonas. Staphylococcus aureus has small number of cultures. These bacterial pathogens show resistant to most of the commonly used antibiotics. The resistant pattern was high in both gram negative and gram positive bacteria. Some organisms show multi-drug resistant pattern. Key words: No growth, bacterial, patients, genera.
Performance of molecular and serologic tests for the diagnosis of scrub typhus

Diagnosis of scrub typhus, caused by the bacterium Orientia tsutsugamushi, is challenging because of the overlap of its non-specific symptoms with other infections coupled with the lack of sufficient data on the performance of diagnostic tests. Early diagnosis of scrub typhus is crucial to improve outcomes and this study evaluates the diagnostic performance of various tests. The present study aims at assessing the accuracy of various rapid diagnostic tests, serologic tests, and nucleic acid amplification methods on well-characterized patient samples. Adult patients with acute febrile illness and manifestations suggestive of scrub typhus confirmed by positive PCR in the blood, eschar or tissue were characterized as cases. Patients with acute febrile illness and a confirmed alternate etiology such as culture-confirmed typhoid, smear/PCR positive for malaria, PCR/NS1 antigen positive for dengue, PCR positive for influenza, PCR/MAT positive for leptospirosis, PCR positive for spotted fever were characterized as controls with other infections. The healthy controls consisted of subjects from the same geographic region. We performed the following tests on blood samples for scrub typhus and calculated the sensitivity, specificity, positive predictive value, and negative predictive value: (1) Quantitative real time PCR using 47kDa gene (qPCR); (2) Conventional PCR using 56kDa gene (cPCR); (3) Loop-mediated isothermal amplification assay (LAMP assay); (4) Immunofluorescence assay (IFA); (5) Enzyme-linked immunosorbent assay (ELISA); (6) Weil-Felix test(WF test); and (7) Immunochromatographic Rapid Diagnostic Test (RDT). Among the 316 participants, 158 had confirmed scrub typhus (cases) and 158 were controls. ELISA and RDT detecting Orientia tsutsugamushi specific IgM antibodies had excellent discriminative potential with sensitivities and specificities of 92%, 94% and 92%, 92% respectively. The sensitivity and specificity of IFA were found to be 95% and 74% respectively. IgM serology had a false positivity rate of 8% with other acute febrile illnesses such as dengue, leptospirosis and spotted fever due to the nonspecific binding of the pentavalent IgM. LAMP assay had 91.7% sensitivity and 77.2% specificity while qPCR provided excellent sensitivity (97%) and perfect specificity. In conclusion, ELISA and RDT detecting Orientia tsutsugamushi specific IgM antibodies have excellent sensitivity and specificity while the accuracy of IFA is suboptimal for the diagnosis of scrub typhus. Given its perfect specificity and superior sensitivity, qPCR is preferred for diagnostic confirmation in reference laboratories particularly for diagnosis of early disease with less than 7 days duration. This study provides a comprehensive evaluation of all currently available diagnostic tests for scrub typhus.
Combined Effect of Naturally-Derived Biofilm Inhibitors and Differentiated HL-60 Cells in the Prevention of Staphylococcus aureus Biofilm Formation

Nosocomial diseases represent a huge health and economic burden. A significant portion is associated with the use of medical devices, with 80% of these infections being caused by a bacterial biofilm. The insertion of a foreign material usually elicits inflammation, which can result in hampered antimicrobial capacity of the host immunity due to the effort of immune cells being directed to degrade the material. The ineffective clearance by immune cells is a perfect opportunity for bacteria to attach and form a biofilm. In this study, we analyzed the antibiofilm capacity of three naturally derived biofilm inhibitors when combined with immune cells in order to assess their applicability in implantable titanium devices and low-density polyethylene (LDPE) endotracheal tubes. To this end, we used a system based on the coculture of HL-60 cells differentiated into polymorphonuclear leukocytes (PMNs) and Staphylococcus aureus (laboratory and clinical strains) on titanium, as well as LDPE surfaces. Out of the three inhibitors, the one coded DHA1 showed the highest potential to be incorporated into implantable devices, as it displayed a combined activity with the immune cells, preventing bacterial attachment on the titanium and LDPE. The other two inhibitors seemed to also be good candidates for incorporation into LDPE endotracheal tubes.
Factors associated with the transition from suicidal ideation to suicide attempt in prison

Abstract Background Although research has identified a wide range of risk factors for suicidal behavior in prisoners, it does not establish who is most likely to act on their suicidal thoughts while incarcerated. Methods Self-report data were collected from a random sample of 1,203 adult men incarcerated across 15 prisons in Belgium, who represent 12% of all male prisoners nationwide. Results One-third (33%) of participants reported having suicidal thoughts during their incarceration, of whom 26% attempted suicide in prison (9% of all prisoners). Factors independently associated with suicide attempt among prisoners with suicidal ideation were violent offending (adjusted odds ratio [aOR] = 2.64, 95% confidence interval [CI] 1.33–5.23), in-prison drug use (aOR = 2.30, 95% CI 1.25–4.22), exposure to suicidal behavior (aOR = 1.96, 95% CI 1.04–3.68), and a lifetime history of nonsuicidal self-injury (aOR = 1.90, 95% CI 1.08–3.36). While related to suicidal thoughts, markers of psychiatric morbidity and aspects of the prison regime were not associated with the progression to suicide attempt. Conclusions Many prisoners who think about suicide do not attempt suicide while incarcerated. Factors associated with suicidal ideation are distinct from those that govern the transition to suicidal behavior. Our findings lend support to the hypothesis that behavioral disinhibition might act as a catalyst in the translation of suicidal thoughts into action.
Comparing machine and deep learning‐based algorithms for prediction of clinical improvement in psychosis with functional magnetic resonance imaging

Previous work using logistic regression suggests that cognitive control‐related frontoparietal activation in early psychosis can predict symptomatic improvement after 1 year of coordinated specialty care with 66% accuracy. Here, we evaluated the ability of six machine learning (ML) algorithms and deep learning (DL) to predict “Improver” status (>20% improvement on Brief Psychiatric Rating Scale [BPRS] total score at 1‐year follow‐up vs. baseline) and continuous change in BPRS score using the same functional magnetic resonance imaging‐based features (frontoparietal activations during the AX‐continuous performance task) in the same sample (individuals with either schizophrenia (n = 65, 49M/16F, mean age 20.8 years) or Type I bipolar disorder (n = 17, 9M/8F, mean age 21.6 years)). 138 healthy controls were included as a reference group. “Shallow” ML methods included Naive Bayes, support vector machine, K Star, AdaBoost, J48 decision tree, and random forest. DL included an explainable artificial intelligence (XAI) procedure for understanding results. The best overall performances (70% accuracy for the binary outcome and root mean square error = 9.47 for the continuous outcome) were achieved using DL. XAI revealed left DLPFC activation was the strongest feature used to make binary classification decisions, with a classification activation threshold (adjusted beta = .017) intermediate to the healthy control mean (adjusted beta = .15, 95% CI = −0.02 to 0.31) and patient mean (adjusted beta = −.13, 95% CI = −0.37 to 0.11). Our results suggest DL is more powerful than shallow ML methods for predicting symptomatic improvement. The left DLPFC may be a functional target for future biomarker development as its activation was particularly important for predicting improvement.
Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells

Ligand-activated glucocorticoid receptor (GR) elicits variable glucocorticoid-modulated transcriptomes in different cell types. However, some genes, including Krüppel-like factor 9 (KLF9), a putative transcriptional repressor, demonstrate conserved responses. We show that glucocorticoids induce KLF9 expression in the human airways in vivo and in differentiated human bronchial epithelial (HBE) cells grown at air–liquid interface (ALI). In A549 and BEAS-2B pulmonary epithelial cells, glucocorticoids induce KLF9 expression with similar kinetics to primary HBE cells in submersion culture. A549 and BEAS-2B ChIP-seq data reveal four common glucocorticoid-induced GR binding sites (GBSs). Two GBSs mapped to the 5ʹ-proximal region relative to KLF9 transcription start site (TSS) and two occurred at distal sites. These were all confirmed in primary HBE cells. Global run-on (GRO) sequencing indicated robust enhancer RNA (eRNA) production from three of these GBSs in BEAS-2B cells. This was confirmed in A549 cells, plus submersion, and ALI culture of HBE cells. Cloning each GBS into luciferase reporters revealed glucocorticoid-induced activity requiring a glucocorticoid response element (GRE) within each distal GBS. While the proximal GBSs drove modest reporter induction by glucocorticoids, this region exhibited basal eRNA production, RNA polymerase II enrichment, and looping to the TSS, plausibly underlying constitutive KLF9 expression. Post glucocorticoid treatment, interactions between distal and proximal GBSs and the TSS correlated with KLF9 induction. CBP/P300 silencing reduced proximal GBS activity, but negligibly affected KLF9 expression. Overall, a model for glucocorticoid-mediated regulation of KLF9 involving multiple GBSs is depicted. This work unequivocally demonstrates that mechanistic insights gained from cell lines can translate to physiologically relevant systems.
Health Care Providers’ Perceptions of Quality, Acceptance, and Satisfaction With Telebehavioral Health Services During the COVID-19 Pandemic: Survey-Based Study

Background Due to rapidly increasing rates of COVID-19 across the country, system-wide changes were needed to protect the health and safety of health care providers and consumers alike. Technology-based care has received buy-in from all participants, and the need for technological assistance has been prioritized. Objective The objective of this study was to determine the initial perceptions and experiences of interprofessional behavioral health providers about shifting from traditional face-to-face care to virtual technologies (telephonic and televideo) during the COVID-19 pandemic. Methods A survey-based study was performed at a large, integrated medical health care system in West-Central Florida that rapidly implemented primary care provision via telephone and televideo as of March 18, 2020. A 23-item anonymous survey based on a 7-point Likert scale was developed to determine health care providers’ perceptions about telephonic and televideo care. The survey took 10 minutes to complete and was administered to 280 professionals between April 27 and May 11, 2020. Results In all, 170 respondents completed the survey in entirety, among which 78.8% (134/170) of the respondents were female and primarily aged 36-55 years (89/170, 52.4%). A majority of the respondents were outpatient-based providers (159/170, 93.5%), including psychiatrists, therapists, counselors, and advanced practice nurses. Most of them (144/170, 84.7%) had used televideo for less than 1 year; they felt comfortable and satisfied with either telephonic or televideo mode and that they were able to meet the patients’ needs. Conclusions Our survey findings suggest that health care providers valued televideo visits equally or preferred them more than telephonic visits in the domains of quality of care, technology performance, satisfaction of technology, and user acceptance.
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.
The Unexplored Virome of Two Atlantic Coast Fish: Contribution of Next-Generation Sequencing to Fish Virology

Much of the knowledge on viruses is focused on those that can be propagated using cell-cultures or that can cause disease in humans or in economically important animals and plants. However, this only reflects a small portion of the virosphere. Therefore, in this study, we explore by targeted next-generation sequencing, how the virome varies between Atlantic horse mackerels and gilthead seabreams from fisheries and aquaculture from the center and south regions of Portugal. Viral genomes potentially pathogenic to fish and crustaceans, as well as to humans, were identified namely Astroviridae, Nodaviridae, Hepadnaviridae, Birnaviridae, Caliciviridae, and Picornaviridae families. Also bacteriophages sequences were identified corresponding to the majority of sequences detected, with Myoviridae, Podoviridae, and Siphoviridae, the most widespread families in both fish species. However, these findings can also be due to the presence of bacteria in fish tissues, or even to contamination. Overall, seabreams harbored viruses from a smaller number of families in comparison with mackerels. Therefore, the obtained data show that fish sold for consumption can harbor a high diversity of viruses, many of which are unknown, reflecting the overall uncharacterized virome of fish. While cross-species transmission of bonafide fish viruses to humans is unlikely, the finding of human pathogenic viruses in fish suggest that fish virome can be a potential threat regarding food safety.
Modelling the Perception of Colour Patterns in Vertebrates with HMAX

In order to study colour signals as animals perceive them, visual ecologists usually rely on models of colour vision that do not consider patterns–the spatial arrangement of features within a signal. HMAX describes a family of models that are used to study pattern perception in human vision research, and which have inspired many artificial intelligence algorithms. In this article, we highlight that the sensory and brain mechanisms modelled in HMAX are widespread, occurring in most if not all vertebrates, thus offering HMAX models a wide range of applications in visual ecology. We begin with a short description of the neural mechanisms of pattern perception in vertebrates, emphasizing similarities in processes across species. Then, we provide a detailed description of HMAX, highlighting how the model is linked to biological vision. We further present sparse-HMAX, an extension of HMAX that includes a sparse coding scheme, in order to make the model even more biologically realistic and to provide a tool for estimating efficiency in information processing. In an illustrative analysis, we then show that HMAX performs better than two other reference methods (manually-positioned landmarks and the SURF algorithm) for estimating similarities between faces in a nonhuman primate species. This manuscript is accompanied with MATLAB codes of an efficient implementation of HMAX and sparse-HMAX that can be further flexibly parameterized to model non-human colour vision, with the goal to encourage visual ecologists to adopt tools from computer vision and computational neuroscience.
CC Chemokines in a Tumor: A Review of Pro-Cancer and Anti-Cancer Properties of the Ligands of Receptors CCR1, CCR2, CCR3, and CCR4

CC chemokines, a subfamily of 27 chemotactic cytokines, are a component of intercellular communication, which is crucial for the functioning of the tumor microenvironment. Although many individual chemokines have been well researched, there has been no comprehensive review presenting the role of all known human CC chemokines in the hallmarks of cancer, and this paper aims at filling this gap. The first part of this review discusses the importance of CCL1, CCL3, CCL4, CCL5, CCL18, CCL19, CCL20, CCL21, CCL25, CCL27, and CCL28 in cancer. Here, we discuss the significance of CCL2 (MCP-1), CCL7, CCL8, CCL11, CCL13, CCL14, CCL15, CCL16, CCL17, CCL22, CCL23, CCL24, and CCL26. The presentation of each chemokine includes its physiological function and then the role in tumor, including proliferation, drug resistance, migration, invasion, and organ-specific metastasis of tumor cells, as well as the effects on angiogenesis and lymphangiogenesis. We also discuss the effects of each CC chemokine on the recruitment of cancer-associated cells to the tumor niche (eosinophils, myeloid-derived suppressor cells (MDSC), tumor-associated macrophages (TAM), tumor-associated neutrophils (TAN), regulatory T cells (Treg)). On the other hand, we also present the anti-cancer properties of CC chemokines, consisting in the recruitment of tumor-infiltrating lymphocytes (TIL).
Lymphoplasmacytic lymphoma associated with diffuse large B-cell lymphoma: Progression or divergent evolution?

Aim Lymphoplasmacytic lymphoma (LPL) is an indolent mature B-cell-neoplasm with involvement of the bone marrow. At least 90% of LPLs carry MYD88-L265P mutation and some of them (~10%) transform into diffuse large B-cell-lymphoma (DLBCL). Material and methods Over the past 15 years we have collected 7 cases where the both LPL and DLBCL were diagnosed in the same patient. Clinical records, analytical data and histopathological specimens were reviewed. FISH studies on paraffin-embedded tissue for MYC, BCL2 and BCL6 genes were performed, as well as MYD88-L265P mutation and IGH rearrangement analysis by PCR. A mutational study was done by massive next generation sequencing (NGS). Results There were 4 women and 3 men between 36–91 years of age. Diagnoses were made simultaneously in 4 patients. In two cases the LPL appeared before the DLBCL and in the remaining case the high-grade component was discovered 5 years before the LPL. In 6 cases both samples shared the MYD88-L265P mutation. IGH rearrangement analysis showed overlapping features in two of 6 cases tested. Mutational study was evaluable in three cases for both samples showing shared and divergent mutations. Conclusions These data suggest different mechanisms of DLBCL development in LPL patients.
The effect of acute, moderate intensity indoor cycling on the temporal resolution of human vision system, measured by critical fusion frequency

Critical fusion frequency (CFF) reflects the basic temporal function of the visual system and therefore is a good measure of its performance. CFF has been implemented in psychological and pharmacological studies to evaluate cognitive functions. The influence of abnormal environmental conditions, such as physical exercise, has been recently explored. Previous studies have presented alterations of cognitive processes due to acute exercise. However, the duration of the effect after the end of exercise has not been investigated. This evaluation is important especially in reference to long‐term conclusions on the effect of training on CFF as an improvement of cognition. The main goal of this study was to check whether a stimulatory effect of acute submaximal physical exercise on CFF among non‐experienced cyclists persists over time. Moreover, we asked whether this effect differs between areas of visual field. CFF thresholds from 15 volunteers were measured by means of an automated medical perimeter PTS 910 (Bogdani) before, immediately after the end, and 30 min after the end of two sessions (training and rest). During rest, CFF did not change significantly, but we observed an increased CFF immediately after training. Interestingly, this increase was maintained 30 min after the end of exercise in fovea. A greater decrease of CFF during rest was observed for lower than for upper hemifield. Our results suggest that an acute, moderate‐intensity cycling improved CFF in non‐experienced cyclists, with the duration of the effect depending on eccentricity. The possible visual hemifield asymmetries of CFF changes over time will be further investigated.