Miracle-dz/UniFAR-FTUs huggingface dataset:
Population background exploration and genetic distribution analysis of Pakistan Hazara via 23 autosomal STRs

Abstract Background: Short tandem repeats (STRs) have gained considerable attention in family search (Y-chromosomal STRs), complex paternity identification (X-chromosomal STRs), routine forensic personal identification (autosomal STRs) and population genetics. Aim: To explore the forensic characteristics of 23 autosomal STRs included in the Huaxia Platinum system in the South Pakistan Hazara population and investigate the genetic similarities and differences between Hazara and 54 worldwide reference populations. Subjects and methods: Variation of the 23 autosomal STRs included in the Huaxia Platinum system was first investigated and reported in a sample of 261 Quetta Hazara in Balochistan Province, Southwest Pakistan. Results: The combined power of discrimination is 0.999999999999999999999999999 and combined power of exclusion is 0.99999999989596 in Quetta Hazara. Comprehensive population comparisons between Hazara and another 13 Eurasian populations based on genotype data, as well as between Hazara and 54 worldwide populations based on the allele frequency distribution, were conducted. Multidimensional scaling plots, principal component analysis, and neighbour-joining phylogenetic trees consistently demonstrated that Pakistan Hazara harbours close affinities with neighbouring Turkic-speaking populations. Model-based genetic structure analysis further suggests that Quetta Hazara derives about half its ancestry directly from the East Asians. Conclusion: Twenty-five forensic-related markers included in the Huaxia Platinum system can be used for forensic practice in the Central Asia Hazara population. Quetta Hazara has a close genetic relationship with the Turkic-speaking populations of Uyghur and Kazakh. Further whole-genome sequencing of Hazara needs to be conducted to validate the observed genetic structure and reconstruct the fine-scale population history of Hazara.
Longitudinal Associations between Sleep, Intrusive Thoughts, and Alcohol Problems Among Veterans.

BACKGROUND Research suggests bidirectional associations between symptoms of posttraumatic stress disorder (PTSD) and sleep disturbance, both of which have been associated with alcohol problems. However, few studies have examined the interplay of these conditions in predicting alcohol problems over time. This study tested 2 competing models: (i) sleep disturbance as a mediator of the association between intrusive thoughts about trauma and alcohol problems and (ii) intrusion symptoms as the mediator of the sleep/alcohol problem association. METHODS Veterans (N = 325, 93% male, 81% White) completed assessments at baseline, 6 months, and 12 months as part of a larger observational study. Zero-inflated-negative binomial models were used to examine indirect effects of baseline predictors on (i) yes/no likelihood and (ii) number of 12-month alcohol problems through 6-month mediators. Models controlled for past-year cannabis use and drinks consumed per week at baseline. RESULTS The only significant predictor of alcohol problem likelihood was baseline drinking quantity. Baseline PTSD intrusions had a direct effect on number of alcohol problems at 12 months, with no indirect (mediated) effect through 6-month sleep disturbance. In the competing model, baseline sleep disturbance had a marginally significant direct effect on 12-month alcohol problems, with a significant indirect effect through 6-month PTSD intrusions. CONCLUSIONS PTSD intrusions are associated with more alcohol problems and help explain the long-term association between sleep and alcohol problems among veterans. Because sleep disturbances are associated with more intrusive thoughts about trauma, we recommend that treatments targeting sleep in the context of PTSD and alcohol use include a cognitive component.
Ten simple rules to create biological network figures for communication

Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule.
CCL28 promotes locomotor recovery after spinal cord injury via recruiting regulatory T cells

Background: Chemokines play a key role in post-traumatic inflammation and secondary injury after spinal cord injury (SCI). CCL28, the chemokine CC-chemokine ligand 28, is involved in the epithelial and mucosal immunity. However, whether CCL28 participates in the physiopathologic processes after SCI remains unclear. Results: CCL28 is upregulated in the spinal cord after SCI. In addition, neutralizing antibodies against IL-1β or TNF-α, or treatment of ML120B, a selective inhibitor of IKK-β, remarkably decrease CCL28 upregulation, suggesting that CCL28 upregulation relies on NF-κB pathway activated by IL-1β and TNF-α after SCI. Moreover, CD4+CD25+FOXP3+ regulatory T (Treg) cells that express CCR10, a receptor of CCL28, are enriched in the spinal cord after SCI. We further demonstrate that the spinal cord recruits Treg cells through CCL28-CCR10 axis, which in turn function to suppress immune response and promote locomotor recovery after SCI. In contrast, neutralizing CCL28 or CCR10 reduces Treg cell recruitment and delays locomotor recovery. Methods: The neutralizing antibodies and recombinant CCL28 were injected intraspinally into the mice prior to SCI, which was established via hemitransection. RT-qPCR analysis was performed to determine transcript level, and Western blot analysis and ELISA assay were used to detect protein expression. Immune cells were analyzed by flow cytometry and visualized by immunofluorescence. The chemotaxis was assessed by in vitro transwell migration assay. The mouse locomotor activity was assessed via the Basso Mouse Scale (BMS) system. Conclusions: These results indicate that NF-κB pathway-regulated CCL28 production plays a protective role after SCI through recruiting CCR10-expressing and immunosuppressive Treg cells, and suggest that interfering CCL28-CCR10 axis might be of potential clinical benefit in improving SCI recovery.
Floral Traits Predict Frequency of Defecation on Flowers by Foraging Bumble Bees

Abstract Flowers may become inoculated with pathogens that can infect bees and other critical pollinators, but the mechanisms of inoculation remain unclear. During foraging, bees may regurgitate or defecate directly onto flower parts, which could inoculate flowers with pollinator pathogens and lead to subsequent disease transmission to floral visitors. We tested if captive eastern bumble bees (Bombus impatiens) (Cresson) (Hymenoptera: Apidae) defecate on floral surfaces during foraging and if flower shape played a role in the probability of defecation and the quantity of feces deposited on floral surfaces. Captive Bombus impatiens were fed a solution of fluorescent dye and sucrose, then allowed to forage freely on flowers of a variety of shapes in a flight cage. Flowers were then examined under ultraviolet light for fluorescing fecal matter. We found that bumble bees did defecate on floral surfaces during foraging and that composite flowers with a large area of disk flowers were the most likely to have feces on them. Our results point to defecation by bumble bees during foraging as a potential mechanism for inoculation of flowers with pollinator pathogens and suggest that flower shape could play a significant role in inoculation.
Anogenital distance in children born of mothers with polycystic ovary syndrome the Odense Child Cohort

STUDY QUESTION: Are higher testosterone levels during pregnancy in women with polycystic ovary 21 syndrome (PCOS) associated with longer offspring anogenital distance (AGD)? SUMMARY AGD was similar in 3-month-old children born of mothers with PCOS compared to controls. ( this section was because it must be a single sentence, and a direct answer of the study WIDER IMPLICATIONS OF THE FINDINGS: Our finding of the same AGD in girls born of mothers with PCOS compared to controls expands previous results of studies reporting longer AGD in adult women with PCOS. Our results suggest that longer AGD in adult women with PCOS could be the result of increased testosterone levels in puberty, perhaps in combination with weight gain.
PAS Domain Containing Repressor 1 (PASD1) Promotes Glioma Cell Proliferation Through Inhibiting Apoptosis In Vitro

Background PAS domain containing repressor 1 (PASD1), the cancer-testis antigen (CTA), has been reported to be aberrantly expressed in various cancer tissues and cancer cell lines; however, normal PASD1 expression can be detected in normal tissue, excluding testicular tissue. Moreover, PASD1 is reported to be abnormally expressed in various malignant tumors. However, it remains unclear whether PASD1 participates in tumorigenesis of glioma. Material/Methods PASD1 expression was detected by immunohistochemistry in 155 glioma tissue specimens in this study. Furthermore, the relationship of PASD1 expression with clinicopathological features in glioma cases was statistically analyzed. In addition, PASD1 was knocked down by small interference RNA (shRNA) in glioma cell line (LN229), so as to assess the potential to use it as the target for treating glioma. Results Our findings suggested that PASD1 expression in glioma patients was extremely upregulated compared with that in normal tissue samples and cell lines. Moreover, PASD1 expression was found to be markedly correlated with gender, The World Health Organization grade and p53 expression; in addition, high PASD1 expression indicated poor prognosis for glioma patients. Additionally, downregulation of PASD1 inhibited the proliferation ability of cells and resulted in cell arrest at the G2/M phase, which was achieved through accelerating apoptosis. Furthermore, our results indicated that PASD1 downregulation could upregulate some apoptosis-modulating proteins at the same time it downregulated some cycle-regulating proteins. Conclusions Taken together, our findings demonstrated that PASD1, an oncogene, can potentially serve as an independent prognostic factor for glioma patients.
The repertory grid game-based learning: a knowledge engineering technique embedded in RPG game-engine

In this paper, the knowledge construction technique called the repertory grid mind tool and the role-playing game (RPG) are used together in a game-based learning activity. The game has been designed and developed for the students in the Faculty of Science and Technology to practice the observation of the important features of birds in the Frugivores and Insectivores. The important features such as foot, leg, beak, crown, and tail are commonly used in the bird observation practice. By giving the hints in the RPG and the embedded repertory grid, students can share their knowledges and construct what they have learned during the game playing process. To evaluate the effectiveness of the game, the study has been tested in two separating group: one is the controlled group in which the students study and practice in the conventional learning environment without playing the game, whereas the other group has been taught in the collaborative learning environment by using this game. The results show that the repertory grid embedded in the RPG game can promote the students’ learning performance.
Effects of Sulfated Fucans from Laminaria hyperborea Regarding VEGF Secretion, Cell Viability, and Oxidative Stress and Correlation with Molecular Weight

Background: Sulfated fucans show interesting effects in the treatment of ocular diseases (e.g., age-related macular degeneration), depending on their chemical structure. Here, we compared three purified sulfated fucans from Laminaria hyperborea (LH) regarding cell viability, oxidative stress protection, and vascular endothelial growth factor (VEGF) secretion in ocular cells. Methods: High-molecular-weight sulfated fucan (Mw = 1548.6 kDa, Fuc1) was extracted with warm water and purified through ultrafiltration. Lower-molecular-weight samples (Mw = 499 kDa, Fuc2; 26.9 kDa, Fuc3) were obtained by mild acid hydrolysis of ultrapurified sulfated fucan and analyzed (SEC-MALS (Size-exclusion chromatography-Multi-Angle Light Scattering), ICP-MS, and GC). Concentrations between 1 and 100 µg/mL were tested. Cell viability was measured after 24 h (uveal melanoma cell line (OMM-1), retinal pigment epithelium (RPE) cell line ARPE-19, primary RPE cells) via MTT/MTS (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide/3-(4,5-Dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assay. Oxidative stress protection was determined after 24 h (OMM-1, ARPE-19). VEGF secretion was analyzed via ELISA after three days (ARPE-19, RPE). Results: Fuc2 and Fuc3 were antiproliferative for OMM-1, but not for ARPE. Fuc1 protected OMM-1. VEGF secretion was lowered with all fucans except Fuc3 in ARPE-19 and RPE. The results suggest a correlation between molecular weight and biological activity, with efficiency increasing with size. Conclusion: The LH sulfated fucan Fuc1 showed promising results regarding VEGF inhibition and protection, encouraging further medical research.
Effects of FGF14 and NaVβ4 deletion on transient and resurgent Na current in cerebellar Purkinje neurons

Purkinje neurons express voltage-gated Na channels and auxiliary proteins that facilitate rapid firing. White et al. find that Na current in isolated Purkinje cells is unaffected by loss of NaVβ4 subunits, but transient current is briefer and resurgent current is reduced without the FGF14 protein.
Changes in substrate utilization rates during 40 min of walking within the Fatmax range.

BACKGROUND AND AIMS The aim of this study was to evaluate changes in fat oxidation rate during 40 min of continuous exercise and identify the intensity at the highest fat oxidation rate (Fatmax). METHODS A total of 14 sedentary males with age, body height, weight, and BMI averages of 29.3 ± 0.7 years, 178.3 ± 1.7 cm, 81.1 ± 3.9 kg, and 25.4 ± 0.9 kg/m2, respectively, were included in the study. Fatmax was determined using an indirect calorimeter with an incremental treadmill walking test at least after 12 h of fasting. On a separate day, at least after 12 h of fasting, the participants walked for 40 min within their predetermined individual Fatmax heart rate and speed ranges. RESULTS The initial fat oxidation rate was not sustained within the first 16 min of exercise and was reduced; however, carbohydrate oxidation reached a stable level after nearly 10 min. CONCLUSIONS In sedentary individuals, during low-intensity physical activity, fat oxidation rates may not be sustainable as expected from Fatmax testing. Therefore, when exercise is prescribed, one should consider that the fat oxidation rate might decrease in sedentary overweight individuals.
Cerebral Venous Thrombosis: MR Black-Blood Thrombus Imaging with Enhanced Blood Signal Suppression

Twenty-six participants underwent conventional imaging methods followed by 2 randomized black-blood thrombus imaging scans, with a preoptimized DANTE preparation switched on and off, respectively. The signal intensity of residual blood, thrombus, brain parenchyma, normal lumen, and noise on black-blood thrombus images were measured. The thrombus volume, SNR of residual blood, and contrast-to-noise ratio for residual blood versus normal lumen, thrombus versus residual blood, and brain parenchyma versus normal lumen were compared between the 2 black-blood thrombus imaging techniques. The new black-blood thrombus imaging technique provided higher thrombus-to-residual blood contrast-to-noise ratio, significantly lower thrombus volume, and substantially improved diagnostic specificity and agreement with conventional imaging methods. BACKGROUND AND PURPOSE: The residual blood flow artifact is a critical confounder for MR black-blood thrombus imaging of cerebral venous sinus thrombosis. This study aimed to conduct a validation of a new MR black-blood thrombus imaging technique with enhanced blood signal suppression. MATERIALS AND METHODS: Twenty-six participants (13 volunteers and 13 patients) underwent conventional imaging methods followed by 2 randomized black-blood thrombus imaging scans, with a preoptimized delay alternating with nutation for tailored excitation (DANTE) preparation switched on and off, respectively. The signal intensity of residual blood, thrombus, brain parenchyma, normal lumen, and noise on black-blood thrombus images were measured. The thrombus volume, SNR of residual blood, and contrast-to-noise ratio for residual blood versus normal lumen, thrombus versus residual blood, and brain parenchyma versus normal lumen were compared between the 2 black-blood thrombus imaging techniques. Segmental diagnosis of venous sinus thrombosis was evaluated for each black-blood thrombus imaging technique using a combination of conventional imaging techniques as a reference. RESULTS: In the volunteer group, the SNR of residual blood (11.3 ± 2.9 versus 54.0 ± 23.4, P < .001) and residual blood-to-normal lumen contrast-to-noise ratio (7.5 ± 3.4 versus 49.2 ± 23.3, P < .001) were significantly reduced using the DANTE preparation. In the patient group, the SNR of residual blood (16.4 ± 8.0 versus 75.0 ± 35.1, P = .002) and residual blood-to-normal lumen contrast-to-noise ratio (12.4 ± 7.8 versus 68.8 ± 35.4, P = .002) were also significantly lower on DANTE-prepared black-blood thrombus imaging. The new black-blood thrombus imaging technique provided higher thrombus-to-residual blood contrast-to-noise ratio, significantly lower thrombus volume, and substantially improved diagnostic specificity and agreement with conventional imaging methods. CONCLUSIONS: DANTE-prepared black-blood thrombus imaging is a reliable MR imaging technique for diagnosing cerebral venous sinus thrombosis.
Performance of vaginal self-sampling for human papillomavirus testing among women living with HIV in Botswana

In Botswana, where human immunodeficiency virus (HIV) prevalence remains high, cervical cancer is the leading cause of cancer deaths in women. Multiple organizations recommend high-risk human papillomavirus (hr-HPV) testing as a screening tool; however, high coverage may not be feasible with provider-collected samples. We conducted the first assessment of self- versus provider-collected samples for hr-HPV testing in HIV-positive women in Botswana and report prevalence of hr-HPV and histological outcomes. We recruited HIV-positive women ≥25 years attending an HIV clinic in Gaborone. Self- and provider-collected samples from participants were tested for hr-HPV using Cepheid GeneXpert. Women testing positive for any hr-HPV returned for colposcopy. We used unweighted κ statistics to determine hr-HPV agreement. We report that 31 (30%) of 103 women tested positive for any hr-HPV. The most common genotypes were HPV 31/33/35/52/58. Overall agreement between self- and provider-collected samples for any hr-HPV was 92% with a κ of 0.80. Ten of the 30 hr-HPV-positive women attending colposcopy had CIN2+ (33%). In conclusion, in this HIV-positive population, there was excellent agreement between self and provider samples, and self-sampling may play an important role in screening programs in high HIV burden settings with limited resources like Botswana.
Difference in the incidence of cerebrospinal fluid leakage and residual tumors between functional and nonfunctional pituitary adenomas treated by endoscopic transsphenoidal pituitary adenomectomy

Objective This study compared the incidence of cerebrospinal fluid (CSF) leakage and residual tumors between functional and nonfunctional pituitary adenomas treated with the endoscopic endonasal transsphenoidal approach (EETA). Methods All patients underwent endocrine examinations and brain magnetic resonance imaging before and after surgery. The length of admission, incidence of central diabetes insipidus, incidence of CSF leakage, symptom relief, and presence of residual tumors were compared between patients with functional and nonfunctional pituitary adenomas. Results Thirty-eight patients were enrolled, among whom 12 and 26 had functional and nonfunctional pituitary adenomas, respectively. The incidence of CSF leakage was significantly higher in patients with nonfunctional adenomas; a hard or elastic tumor character accounted for the difference. A large tumor size and cavernous sinus invasion were risk factors for residual tumors. No significant differences were found in sex, length of admission, operative times, incidence of diabetes insipidus, or number of residual tumors between the two groups. The hormone levels were lower postoperatively than preoperatively in patients with nonfunctional adenomas. Conclusion Nonfunctional pituitary macroadenomas resulted in more CSF leakage. Use of the rescue nasoseptal flap reduced unnecessary nasal destruction. Cooperation between a neurosurgeon and otolaryngologist was safer and more effective when using the EETA.
Reply to Bracher: Scoring probabilistic forecasts to maximize public health interpretability

Evaluating probabilistic forecasts in the context of a real-time public health surveillance system is a complicated business. We agree with Bracher’s (1) observations that the scores established by the US Centers for Disease Control and Prevention (CDC) and used to evaluate our forecasts of seasonal influenza in the United States are not “proper” by definition (2). We thank him for raising this important issue. A key advantage of proper scoring is that it incentivizes forecasters to provide their best probabilistic estimates of the fundamental unit of prediction. In the case of the FluSight competition targets, the units are intervals or bins containing dates or values representing influenza-like illness (ILI) activity. A forecast assigns probabilities to each bin. During the evolution of the FluSight challenge, the organizers at CDC made a conscious decision to use a “moving window” or “multibin” score that … [↵][1]1To whom correspondence may be addressed. Email: nick{at}schoolph.umass. edu. [1]: #xref-corresp-1-1
Beta power encodes contextual estimates of temporal event probability in the human brain

To prepare for an impending event of unknown temporal distribution, humans internally increase the perceived probability of event onset as time elapses. This effect is termed the hazard rate of events. We tested how the neural encoding of hazard rate changes by providing human participants with prior information on temporal event probability. We recorded behavioral and electroencephalographic (EEG) data while participants listened to continuously repeating five-tone sequences, composed of four standard tones followed by a non-target deviant tone, delivered at slow (1.6 Hz) or fast (4 Hz) rates. The task was to detect a rare target tone, which equiprobably appeared at either position two, three or four of the repeating sequence. In this design, potential target position acts as a proxy for elapsed time. For participants uninformed about the target’s distribution, elapsed time to uncertain target onset increased response speed, displaying a significant hazard rate effect at both slow and fast stimulus rates. However, only in fast sequences did prior information about the target’s temporal distribution interact with elapsed time, suppressing the hazard rate. Importantly, in the fast, uninformed condition pre-stimulus power synchronization in the beta band (Beta 1, 15–19 Hz) predicted the hazard rate of response times. Prior information suppressed pre-stimulus power synchronization in the same band, while still significantly predicting response times. We conclude that Beta 1 power does not simply encode the hazard rate, but—more generally—internal estimates of temporal event probability based upon contextual information.