Miracle-dz/UniFAR-FTUs huggingface dataset:
Mortality and Disability-Adjusted Life-Years (Dalys) for Common Neglected Tropical Diseases in Ethiopia, 1990-2015: Evidence from the Global Burden of Disease Study 2015.

INTRODUCTION Neglected tropical diseases (NTDs) are important public health problems in Ethiopia. In 2013, the Federal Ministry of Health (FMOH) has launched a national NTD master plan to eliminate major NTDs of public health importance by 2020. Benchmarking the current status of NTDs in the country is important to monitor and evaluate the progress in the implementation of interventions and their impacts. Therefore, this study aims to assess the trends of mortality and Disability-adjusted Life-Years (DALY) for the priority NTDs over the last 25 years. METHODS We used the Global Burden of Disease (GBD) 2015 estimates for this study. The GBD 2015 data source for cause of death and DALY estimation included verbal autopsy (VA), Demographic and Health Surveys (DHS), and other disease specific surveys, Ministry of Health reports submitted to United Nations (UN) agencies and published scientific articles. Cause of Death Ensemble modeling (CODEm) and/or natural history models were used to estimate NTDs mortality rates. DALY were estimated as the sum of Years of Life Lost (YLL) due to premature mortality and Years Lived with Disability (YLD). RESULTS All NTDs caused an estimated of 6,293 deaths (95% uncertainty interval (UI): 3699-10,080) in 1990 and 3,593 deaths (95% UI: 2051 - 6178) in 2015, a 43% reduction over the 25 years. Age-standardized mortality rates due to schistosomiasis, STH and leshmaniasis have declined by 91.3%, 73.5% and 21.6% respectively between 1990 to 2015. The number of DALYs due to all NTDs has declined from 814.4 thousand (95% UI: 548 thousand-1.2million) in 1990 to 579.5 thousand (95%UI: 309.4 thousand-1.3 million) in 2015. Age-standardized DALY rates due to all NTDs declined by 30.7%, from 17.6 per 1000(95%UI: 12.5-26.5) in 1990 to 12.2 per 1000(95%UI: 6.5 - 27.4) in 2015. Age-standardized DALY rate for trachoma declined from 92.7 per 100,000(95% UI: 63.2 - 128.4) in 1990 to 41.2 per 100,000(95%UI: 27.4-59.2) in 2015, a 55.6% reduction between 1990 and 2015. Age-standardized DALY rates for onchocerciasis, schistosomiasis and lymphiaticfilariasis decreased by 66.2%, 29.4% and 12.5% respectively between 1990 and 2015. DALY rate for ascariasis fell by 56.8% over the past 25 years. CONCLUSIONS Ethiopia has made a remarkable progress in reducing the DALY rates for most of the NTDs over the last 25 years. The rapid scale of interventions and broader system strengthening may have a lasting impact on achieving the 2020 goal of elimination of most of NTDs. Ethiopia should strengthen the coverage of integrated interventions of NTD through proper coordination with other health programs and sectors and community participation to eliminate NTDs by 2020.
Residential mobility and ethnic segregation in Stockholm

Social science research has been concerned with various aspects of residential segregation and why aggregate patterns of segregation emerge and become established in urban areas. This thesis aims at gaining a deeper understanding of which mechanisms influence patterns of residential segregation by examining people’s mobility behavior. People’s residential mobility behavior is a crucial factor for understanding outcomes of segregation on the aggregate level. By both including individual and neighborhood characteristics in the analysis, more insight is gained in how ethnic and socioeconomic compositions of neighborhoods affect individuals’ mobility decisions. Swedish register data from 1990-2006 is used to estimate neighborhood choice models for the greater Stockholm area. The results show that individuals are likely to choose neighborhoods in which the population is similar to themselves, regarding both migrant background and income. The analyses also find some limited support for mechanisms of native-flight and avoidance when looking at Swedes’ mobility behavior. Nevertheless, economic resources seem to be of more relative importance for Swedes' and immigrants' neighborhood choice than the percentage of migrant groups living in a neighborhood.
Radiation therapy improves survival in patients with testicular diffuse large B-cell lymphoma*

Abstract In 120 Stage I–IV testicular diffuse large B-cell lymphoma (DLBCL) patients treated from 1964 to 2015, we assessed the benefits of prophylactic contralateral testicular radiation (RT) and prophylactic central nervous system (CNS) therapy on overall, progression free, testicular relapse free, and CNS relapse free survival (OS, PFS, TRFS, and CRFS, respectively). Seventy percent of patients received RT, 53% received anthracyclines and rituximab (modern therapy), and 61% received CNS prophylaxis. On univariate analysis RT was associated with improved TRFS, PFS, and trended toward improved OS. On multivariate analysis (MVA), RT was significantly associated with improved OS and PFS; the PFS benefit persisted among patients receiving modern therapy. CNS prophylaxis was associated with improved OS, PFS, and TRFS, but not CRFS on univariate analysis, and was not significant on MVA. RT is associated with improved survival, and should be considered for all testicular DLBCL patients, but additional strategies are needed to prevent CNS relapse.
DNA preservation: a test of commonly used preservatives for insects

Abstract. Understanding the impact of collection and storage preservatives is important for all specimen-based research, ranging from morphological studies to genetic- and genomic-based research. We evaluated the effectiveness of four commonly used preservatives for their ability to preserve insect DNA for several ant species as well as the DNA from host-associated microbes of one ant species. We made replicated collections of ant specimens of different sizes and from three different environmental climates into four different preservatives (95% ethanol, dimethyl sulfoxide (DMSO), propylene glycol and RNAlater), isolated DNA across two different time periods and performed PCR on all DNA extracts (n = 180 samples + 10 controls). Although ethanol returned the best overall results for DNA yield and PCR success, our analyses did not show a significant difference between specimens preserved in ethanol or propylene glycol on the timescales we investigated. We found that average DNA yield was significantly higher when specimens were originally collected in ethanol instead of DMSO, propylene glycol, or RNAlater™ (Applied Biosystems/Ambion). PCR results for both the insect and endosymbiotic bacteria showed a significant advantage for preserving ants in ethanol or propylene glycol over DMSO or RNAlater for room temperature storage. Our findings suggest that collection of insect specimens into ethanol is the preferred method for preserving host and host-associated bacterial DNA, but that propylene glycol is a suitable alternative when ethanol is not available or permitted.
High-Dose Radiation as a Dramatic, Immunological Primer in Locally Advanced Melanoma

A 53-year-old white male presented with a right axillary melanoma that became widely metastatic and progressive despite multiple systemic treatments. He became refractory to ipilimumab (Yervoy) and pembrolizumab (Keytruda). He presented with a very large, painful left posterior neck mass that was 18 x 15 x 8 cm in size clinically. He was treated with a single fraction of 20 Gy using parallel opposed, spatially fractionated GRID radiation therapy (SFGRT), along with concurrent pembrolizumab. He also received 50 Gy in 25 fractions of conventional radiation. After five months of concurrent treatment, the refractory neck mass had completely resolved and he had no lasting side effects. Our dramatic case confirms the synergistic effect of high-dose GRID radiation as a primer for renewed, enhanced immunological response, and we have used this approach successfully on a number of similar patients with rapid and durable results.
Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology

Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10−8) for cranial base width at 14q21.1 and 20q12, intercanthal width at 1p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.
Linking global climate and temperature variability to widespread amphibian declines putatively caused by disease

The role of global climate change in the decline of biodiversity and the emergence of infectious diseases remains controversial, and the effect of climatic variability, in particular, has largely been ignored. For instance, it was recently revealed that the proposed link between climate change and widespread amphibian declines, putatively caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), was tenuous because it was based on a temporally confounded correlation. Here we provide temporally unconfounded evidence that global El Niño climatic events drive widespread amphibian losses in genus Atelopus via increased regional temperature variability, which can reduce amphibian defenses against pathogens. Of 26 climate variables tested, only factors associated with temperature variability could account for the spatiotemporal patterns of declines thought to be associated with Bd. Climatic predictors of declines became significant only after controlling for a pattern consistent with epidemic spread (by temporally detrending the data). This presumed spread accounted for 59% of the temporal variation in amphibian losses, whereas El Niño accounted for 59% of the remaining variation. Hence, we could account for 83% of the variation in declines with these two variables alone. Given that global climate change seems to increase temperature variability, extreme climatic events, and the strength of Central Pacific El Niño episodes, climate change might exacerbate worldwide enigmatic declines of amphibians, presumably by increasing susceptibility to disease. These results suggest that changes to temperature variability associated with climate change might be as significant to biodiversity losses and disease emergence as changes to mean temperature.
The importance of sampling standardization for comparisons of insect herbivory in deep time: a case study from the late Palaeozoic

Sampling standardization has not been fully addressed for the study of insect herbivory in the fossil record. The effects of sampling within a single locality were explored almost a decade ago, but the importance of sampling standardization for comparisons of herbivory across space and time has not yet been evaluated. Here, we present a case study from the Permian in which we evaluate the impact of sampling standardization on comparisons of insect herbivory from two localities that are similar in age and floral composition. Comparisons of insect damage type (DT) diversity change dramatically when the number of leaves examined is standardized by surface area. This finding suggests that surface area should always be taken into account for comparisons of DT diversity. In addition, the three most common metrics of herbivory—DT diversity, proportion of leaves herbivorized and proportion of leaf surface area herbivorized—are inherently decoupled from each other. The decoupling of the diversity and intensity of insect herbivory necessitates a reinterpretation of published data because they had been conflated in previous studies. Future studies should examine the divergent ecological factors that underlie these metrics. We conclude with suggestions to guide the sampling and analysis of herbivorized leaves in the fossil record.
Application of spermatozoa from neo-males (XX) to induce androgenetic development in rainbow trout (Oncorhynchus mykiss)

In species like rainbow trout (Oncorhynchus mykiss) that show male heterogamety (XY), induced androgenesis results in production of females (XX) and males (YY). Morphological and genetic differences between rainbow trout X and Y chromosomes suggest that androgenetic males (YY) may show lower survival than androgenetic females (XX). To test this hypothesis, we produced lines of androgenetic rainbow trout composed of males (YY) and females (XX) and of only females (XX) using spermatozoa from normal males (XY) and neo-males (XX), respectively. Survival rates of the androgenotes were monitored until gonadal differentiation and no significant differences in survival between XX/YY and XX androgenetic rainbow trout lines were observed. Sex-genotypes of the paternal males and androgenetic offspring were confirmed using a rainbow trout Y chromosome-related DNA marker. Histological analysis performed to detect potential disturbances in the gonadal development of the androgenetic XX and YY rainbow trout showed proper development of testes and ovaries in most of the studied individuals. Our results indicated that differences between rainbow trout X and Y chromosomes did not affect survival of the androgenetic offspring. Application of spermatozoa from neo-males to induce androgenetic development may have some potential in rainbow trout aquaculture to produce homozygous females that may be used in breeding programmes and to establish clonal lines.
Stress Granule-Inducing Eukaryotic Translation Initiation Factor 4A Inhibitors Block Influenza A Virus Replication

Eukaryotic translation initiation factor 4A (eIF4A) is a helicase that facilitates assembly of the translation preinitiation complex by unwinding structured mRNA 5’ untranslated regions. Pateamine A (PatA) and silvestrol are natural products that disrupt eIF4A function and arrest translation, thereby triggering the formation of cytoplasmic aggregates of stalled preinitiation complexes known as stress granules (SGs). Here we examined the effects of eIF4A inhibition by PatA and silvestrol on influenza A virus (IAV) protein synthesis and replication in cell culture. Treatment of infected cells with either PatA or silvestrol at early times post-infection results in SG formation, arrest of viral protein synthesis and failure to replicate the viral genome. PatA, which irreversibly binds to eIF4A, sustained long-term blockade of IAV replication following drug withdrawal, and inhibited IAV replication at concentrations that had minimal cytotoxicity. By contrast, the antiviral effects of silvestrol were fully reversible; drug withdrawal caused rapid SG dissolution and resumption of viral protein synthesis. IAV inhibition by silvestrol was invariably associated with cytotoxicity. PatA blocked replication of genetically divergent IAV strains, suggesting common dependence on host eIF4A activity. This study demonstrates the feasibility of targeting core host protein synthesis machinery to prevent viral replication. IMPORTANCE Influenza A virus (IAV) relies on cellular protein synthesis to decode viral messenger RNAs. Pateamine A and silvestrol are natural products that inactivate an essential protein synthesis protein known as eIF4A. Here we show that IAV is sensitive to these eIF4A inhibitor drugs. Treatment of infected cells with pateamine A or silvestrol prevented synthesis of viral proteins, viral genome replication and release of infectious virions. The irreversible eIF4A inhibitor pateamine A sustained long-term blockade of viral replication, whereas viral protein synthesis quickly resumed after silvestrol was removed from infected cells. Prolonged incubation of either infected or uninfected cells with these drugs induced the programmed cell death cascade called apoptosis. Our findings suggest that core components of the host protein synthesis machinery are viable targets for antiviral drug discovery. The most promising drug candidates should selectively block protein synthesis in infected cells without perturbing bystander uninfected cells.
Comprehensive review of stereotactic radiosurgery for medically and surgically refractory pituitary adenomas

Despite advances in surgical techniques and medical therapies, a significant proportion of pituitary adenomas remain endocrinologically active, demonstrate persistent radiographic disease, or recur when followed for long periods of time. While surgical intervention remains the first-line therapy, stereotactic radiosurgery is increasingly recognized as a viable treatment option for these often challenging tumors. In this review, we comprehensively review the literature to evaluate both endocrinologic and radiographic outcomes of radiosurgical management of pituitary adenomas. The literature clearly supports the use of radiosurgery, with endocrinologic remission rates and time to remission varying by tumor type [prolactinoma: 20–30%, growth hormone secreting adenomas: ~50%, adrenocorticotrophic hormone (ACTH)-secreting adenomas: 40–65%] and radiographic control rates almost universally greater than 90% with long-term follow-up. We stratify the outcomes by tumor type, review the importance of prognostic factors (particularly, pre-treatment endocrinologic function and tumor size), and discuss the complications of treatment (with special attention to endocrinopathy and visual complications). We conclude that the literature supports the use of radiosurgery for treatment-refractory pituitary adenomas, providing the patient with a minimally invasive, safe, and effective treatment option for an otherwise resistant tumor. As such, we provide literature-based treatment considerations, including radiosurgical dose, endocrinologic, radiographic, and medical considerations for each adenoma type.
Improving Data Locality for Efficient In‐Core Path Tracing

In this paper, we investigate the efficiency of ray queries on the CPU in the context of path tracing, where ray distributions are mostly random. We show that existing schemes that exploit data locality to improve ray tracing efficiency fail to do so beyond the first diffuse bounce, and analyze the cause for this. We then present an alternative scheme inspired by the work of Pharr et al. in which we improve data locality by using a data‐centric breadth‐first approach. We show that our scheme improves on state‐of‐the‐art performance for ray distributions in a path tracer.
Polymerized-Type I Collagen Induces a High Quality Cartilage Repair in a Rat Model of Osteoarthritis

1 Department of Infectomic and Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional. Av. Instituto Politécnico Nacional, Col. San Pedro Zacatenco, Apdo. Postal 14740, Mexico City, Mexico. 2 Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga No. 15, Col. Belisario Domínguez, Sección XVI, Alcaldía Tlalpan, C.P.14080, Mexico City, Mexico.
Self-efficacy as a marker of cardiac function and predictor of heart failure hospitalization and mortality in patients with stable coronary heart disease: findings from the Heart and Soul Study.

OBJECTIVE The authors sought to evaluate the association of self-efficacy with objective measures of cardiac function, subsequent hospitalization for heart failure (HF), and all-cause mortality. DESIGN Observational cohort of ambulatory patients with stable CHD. The authors measured self-efficacy using a published, validated, 5-item summative scale, the Sullivan Self-Efficacy to Maintain Function Scale. The authors also performed a cardiac assessment, including an exercise treadmill test with stress echocardiography. MAIN OUTCOME MEASURES Hospitalizations for HF, as determined by blinded review of medical records, and all-cause mortality, with adjustment for demographics, medical history, medication use, depressive symptoms, and social support. RESULTS Of the 1,024 predominately male, older CHD patients, 1013 (99%) were available for follow-up, 124 (12%) were hospitalized for HF, and 235 (23%) died during 4.3 years of follow-up. Mean cardiac self-efficacy score was 9.7 (SD 4.5, range 0-20), corresponding to responses between "not at all confident" and "somewhat confident" for ability to maintain function. Lower self-efficacy predicted subsequent HF hospitalization (OR per SD decrease = 1.4, p = .0006), and all-cause mortality (OR per SD decrease = 1.4, p < .0001). After adjustment, the association of cardiac self-efficacy with both HF hospitalization and mortality was explained by worse baseline cardiac function. CONCLUSION Among patients with CHD, self-efficacy was a reasonable proxy for predicting HF hospitalizations. The increased risk of HF associated with lower baseline self-efficacy was explained by worse cardiac function. These findings indicate that measuring cardiac self-efficacy provides a rapid and potentially useful assessment of cardiac function among outpatients with CHD.
Face perception in its neurobiological and social context

Significant advances in the understanding of processes involved in face perception have been achieved. This study aims to review the literature of face perception in neurobiological and social contexts. The review focused on the mechanisms of mediation of face perception by neural substrates, and discussed some of the social signals provided by faces. We showed that psychological, neurophysiological and neuroimaging studies have demonstrated that a dedicated neural system for face perception exists in primates, which includes the fusiform face area (FFA), anterior superior temporal sulcus (STS) and anterior inferior temporal gyrus (ITG). But it remains to be understood how the integration of face perception occurs in the neurobiological context and in the social context.