Miracle-dz/UniFAR-FTUs huggingface dataset:
Terabyte-scale Deep Multiple Instance Learning for Classification and Localization in Pathology

In the field of computational pathology, the use of decision support systems powered by state-of-the-art deep learning solutions has been hampered by the lack of large labeled datasets. Until recently, studies relied on datasets in the order of few hundreds of slides which are not enough to train a model that can work at scale in the clinic. Here, we have gathered a dataset consisting of 12,160 slides, two orders of magnitude larger than previous datasets in pathology and equivalent to 25 times the pixel count of the entire ImageNet dataset. Given the size of our dataset it is possible for us to train a deep learning model under the Multiple Instance Learning (MIL) assumption where only the overall slide diagnosis is necessary for training, avoiding all the expensive pixel-wise annotations that are usually part of supervised learning approaches. We test our framework on a complex task, that of prostate cancer diagnosis on needle biopsies. We performed a thorough evaluation of the performance of our MIL pipeline under several conditions achieving an AUC of 0.98 on a held-out test set of 1,824 slides. These results open the way for training accurate diagnosis prediction models at scale, laying the foundation for decision support system deployment in the clinic.
Imported cases and minimum temperature drive dengue transmission in Guangzhou, China: evidence from ARIMAX model

Abstract Dengue is the fastest spreading mosquito-transmitted disease in the world. In China, Guangzhou City is believed to be the most important epicenter of dengue outbreaks although the transmission patterns are still poorly understood. We developed an autoregressive integrated moving average model incorporating external regressors to examine the association between the monthly number of locally acquired dengue infections and imported cases, mosquito densities, temperature and precipitation in Guangzhou. In multivariate analysis, imported cases and minimum temperature (both at lag 0) were both associated with the number of locally acquired infections (P < 0.05). This multivariate model performed best, featuring the lowest fitting root mean squared error (RMSE) (0.7520), AIC (393.7854) and test RMSE (0.6445), as well as the best effect in model validation for testing outbreak with a sensitivity of 1.0000, a specificity of 0.7368 and a consistency rate of 0.7917. Our findings suggest that imported cases and minimum temperature are two key determinants of dengue local transmission in Guangzhou. The modelling method can be used to predict dengue transmission in non-endemic countries and to inform dengue prevention and control strategies.
A global model of sodium in the mesosphere and lower thermosphere has been developed within the framework of the National Center for Atmospheric Research ’ s Whole Atmosphere Community Climate Model ( WACCM )

[1] A global model of sodium in the mesosphere and lower thermosphere has been developed within the framework of the National Center for Atmospheric Research’s Whole Atmosphere Community Climate Model (WACCM). The standard fully interactive WACCM chemistry module has been augmented with a chemistry scheme that includes nine neutral and ionized sodium species. Meteoric ablation provides the source of sodium in the model and is represented as a combination of a meteoroid input function (MIF) and a parameterized ablation model. The MIF provides the seasonally and latitudinally varying meteoric flux which is modeled taking into consideration the astronomical origins of sporadic meteors and considers variations in particle entry angle, velocity, mass, and the differential ablation of the chemical constituents. WACCM simulations show large variations in the sodium constituents over time scales from days to months. Seasonality of sodium constituents is strongly affected by variations in the MIF and transport via the mean meridional wind. In particular, the summer to winter hemisphere flow leads to the highest sodium species concentrations and loss rates occurring over the winter pole. In the Northern Hemisphere, this winter maximum can be dramatically affected by stratospheric sudden warmings. Simulations of the January 2009 major warming event show that it caused a short-term decrease in the sodium column over the polar cap that was followed by a factor of 3 increase in the following weeks. Overall, the modeled distribution of atomic sodium in WACCM agrees well with both ground-based and satellite observations. Given the strong sensitivity of the sodium layer to dynamical motions, reproducing its variability provides a stringent test of global models and should help to constrain key atmospheric variables in this poorly sampled region of the atmosphere.
Prevalence and factors associated with underutilization of antenatal care services in Nigeria: A comparative study of rural and urban residences based on the 2013 Nigeria demographic and health survey

Introduction Antenatal care (ANC) is a major public health intervention aimed at ensuring safe pregnancy outcomes. In Nigeria, the recommended minimum of four times ANC attendance is underutilized. This study investigates the prevalence and factors associated with underutilization of ANC services with a focus on the differences between rural and urban residences in Nigeria. Methods We analyzed the 2013 Nigeria Demographic and Health Survey dataset with adjustment for the sampling weight and the cluster design of the survey. The prevalence of underutilization of ANC was assessed using frequency tabulation while associated factors were examined using Chi-Square test and multivariable logistic regression analysis. Results The prevalence of underutilization of ANC was 46.5% in Nigeria, 61.1% in rural residence and 22.4% in urban residence. The North-West region had the highest prevalence of ANC underuse in Nigeria at 69.3%, 76.6% and 44.8% for the overall, rural and urban residences respectively. Factors associated with greater odds of ANC underuse in rural residence were maternal non-working status, birth interval < 24 months, single birth type, not listening to radio at all, lack of companionship to health facility and not getting money for health services. In urban residence, mothers professing Islam, those who did not read newspaper at all, and those who lacked health insurance, had greater odds of ANC underuse. In both rural and urban residence, maternal and husband’s education level, region of residence, wealth index, maternal age, frequency of watching television, distance to- and permission to visit health facility were significantly associated with ANC underuse. Conclusions Rural-urban differences exist in the use of ANC services, and to varying degrees, factors associated with underuse of ANC in Nigeria. Interventions aimed at addressing factors identified in this study may help to improve the utilization of ANC services both in rural and urban Nigeria. Such interventions need to focus more on reducing socioeconomic, geographic and regional disparities in access to ANC in Nigeria.
Effects of dietary n-3 fatty acid deficiency and repletion in the guinea pig retina.

PURPOSE To investigate the nature and reversibility of biochemical and functional changes in the retina encountered over a single generation of dietary n-3 polyunsaturated fatty acid deficiency in guinea pigs. METHODS Dunkin-Hartley guinea pigs were fed for 16 weeks after weaning with diets supplemented with safflower seed oil (n-3 deficient) or canola oil (n-3 sufficient, control). A number of deficient animals were repleted at 6 weeks with canola oil for 5 or 10 weeks, or at 11 weeks for 5 weeks. Electroretinograms (0.8 and 4.3 log scot td x sec) were collected at 6, 11, and 16 weeks after weaning. Conventional waveforms (a- and b-waves), oscillatory potentials, and receptoral and postreceptoral subcomponents (PIII and PII, respectively) were evaluated. Cone pathway function was assessed with 30-Hz flicker at the brighter intensity. Retinal phospholipid fatty acids were measured by capillary gas-liquid chromatography. RESULTS Electroretinographic amplitudes showed statistically significant losses in b- and a-waves after 6 and 16 weeks of dietary n-3 deficiency, respectively. The response amplitude to 30-Hz flicker was reduced 42% after 16 weeks. Retinal docosahexaenoic acid (DHA) levels of animals maintained on the safflower oil diet for 16 weeks were 42% of levels in age-matched control subjects. There were significant losses in maximum response amplitudes (R(mPIII) and R(mPII)), although the major effect was a reduction in sensitivity of the receptoral response. Complete functional recovery was observed only in animals repleted for 10 weeks. CONCLUSIONS Functional deficits in PIII and PII of the electroretinogram were apparent in first-generation guinea pigs fed an n-3 deficient diet. These losses showed a correlation with age and retinal DHA level, although varying degrees of dependence on the DHA level were found. All functional deficits were reversed after 10 weeks of dietary n-3 repletion. The results suggest that DHA may serve several functional and structural roles in the retina and further emphasize the requirement for DHA in the normal development of vision.
Influence of Head Teachers’ Supervision of Teacher Curriculum Development on Provision of Quality Education in Secondary Schools in Kenya

Kenya has, since independence desired to provide quality education to learners. Despite the Governments’ efforts to implement measures to improve quality of education in schools, the secondary sub-sector continues to face supervision challenges that could compromise the quality of education provided. The objective of the study was to find out if the head teachers’ curriculum implementation, had any influence on provision of quality education in Kisumu East Sub-County, Kenya. The study population considered 48 secondary schools with a population of 927 students, 449 teachers and 48 head teachers. The study used a sample size of 370 of 309 students, 45 teachers randomly selected and 16 head teachers selected using purposive sampling. The instrument validity was ascertained by use of a four-point scale rating by experienced colleagues to ascertain if the questions were relevant while instrument reliability was ascertained by Test re-test Technique. The research Design was Descriptive Survey. The qualitative data was analyzed using descriptive and inferential statistics. Data from interviews were analyzed qualitatively in an on-going process as the themes and sub-themes emerged from the data. The findings of the study showed that there was a strong relationship between head teacher supervision of curriculum implementation on quality education provision in Kisumu East Sub-county, Kenya. The study concluded that head teachers employed inadequate methods for supervision of teachers in the sampled schools, preferring to rely on written records to establish the quality of education, and reports from HODs. The study recommended that the head teachers should take up their roles as internal quality assurance officers and ensure that they attended supervision training sessions offered by Kenya Educational Management Institute.
Sclerosing peritonitis with unilateral ovarian luteinized thecoma in a post-menopausal woman: A case report

A unique case of unilateral ovarian luteinized thecoma with sclerosing peritonitis is reported because the association between these two conditions is extremely rare. Etiology is not clearly known. A 50-year-old post-menopausal woman presented with pain abdomen and huge swelling. Pelvic contrast-enhanced computed tomography (CECT) revealed a heterogenous enhancing mass arising possibly from ovary and adherent to uterus, bowl loops, and omentum. A spindle cell neoplasm without definite features of malignancy was reported in computed tomography (CT)-guided fine-needle aspiration cytology (FNAC). Ascitic fluid was negative for malignancy. Her serum carcinoembryonic antigen (CEA) (1.1ng/ml) and CA125 (27.6μ/ml) level was within normal limits. Total abdominal hysterectomy with bilateral supracolic omentectomy, resection of part of colon, and supracolic omentectomy was done. Histopathological diagnosis was luteinized thecoma with sclerosing peritonitis. Tumor cells were immunoreactive to smooth muscle antigen (SMA) and CD 99 and non- reactive to ER, PR, Calretinine, and Cytokeratin. Patient developed post-operative sepsis and enterocutaneous fistula, which was managed conservatively and was kept in follow-up. According to current concept, in spite of its large size, wide-spread involvement, mitotic activity, and complications due to peritoneal involvement, behavior of this rare clinical entity is benign.
Drivers potentially influencing host–bat fly interactions in anthropogenic neotropical landscapes at different spatial scales

Abstract The anthropogenic modification of natural landscapes, and the consequent changes in the environmental conditions and resources availability at multiple spatial scales can affect complex species interactions involving key-stone species such as bat–parasite interactions. In this study, we aimed to identify the drivers potentially influencing host–bat fly interactions at different spatial scales (at the host, vegetation stand and landscape level), in a tropical anthropogenic landscape. For this purpose, we mist-netted phyllostomid and moormopid bats and collected the bat flies (streblids) parasitizing them in 10 sites representing secondary and old growth forest. In general, the variation in fly communities largely mirrored the variation in bat communities as a result of the high level of specialization characterizing host–bat fly interaction networks. Nevertheless, we observed that: (1) bats roosting dynamics can shape bat–streblid interactions, modulating parasite prevalence and the intensity of infestation; (2) a degraded matrix could favor crowding and consequently the exchange of ectoparasites among bat species, lessening the level of specialization of the interaction networks and promoting novel interactions; and (3) bat–fly interaction can also be shaped by the dilution effect, as a decrease in bat diversity could be associated with a potential increase in the dissemination and prevalence of streblids.
Silencing of Syntaxin 1A in the Dopaminergic Neurons Decreases the Activity of the Dopamine Transporter and Prevents Amphetamine-Induced Behaviors in C. elegans

The dopamine transporter (DAT) is a cell membrane protein whose main function is to reuptake the dopamine (DA) released in the synaptic cleft back into the dopaminergic neurons. Previous studies suggested that the activity of DAT is regulated by allosteric proteins such as Syntaxin-1A and is altered by drugs of abuse such as amphetamine (Amph). Because Caenorhabditis elegans expresses both DAT (DAT-1) and Syntaxin-1A (UNC-64), we used this model system to investigate the functional and behavioral effects caused by lack of expression of unc-64 in cultured dopaminergic neurons and in living animals. Using an inheritable RNA silencing technique, we were able to knockdown unc-64 specifically in the dopaminergic neurons. This cell-specific knockdown approach avoids the pleiotropic phenotypes caused by knockout mutations of unc-64 and ensures the transmission of dopaminergic specific unc-64 silencing to the progeny. We found that, similarly to dat-1 knockouts and dat-1 silenced lines, animals with reduced unc-64 expression in the dopaminergic neurons did not respond to Amph treatment when tested for locomotor behaviors. Our in vitro data demonstrated that in neuronal cultures derived from animals silenced for unc-64, the DA uptake was reduced by 30% when compared to controls, and this reduction was similar to that measured in neurons isolated from animals silenced for dat-1 (40%). Moreover, reduced expression of unc-64 in the dopaminergic neurons significantly reduced the DA release elicited by Amph. Because in C. elegans DAT-1 is the only protein capable to reuptake DA, these data show that reduced expression of unc-64 in the dopaminergic neurons decreases the capability of DAT in re-accumulating synaptic DA. Moreover, these results demonstrate that decreased expression of unc-64 in the dopaminergic neurons abrogates the locomotor behavior induced by Amph. Taken together these data suggest that Syntaxin-1A plays an important role in both functional and behavioral effects caused by Amph.
Review analysis and impact of co-circulating H5N1 and H9N2 avian influenza viruses in Bangladesh

Abstract Almost the full range of 16 haemagglutinin (HA) and nine neuraminidase subtypes of avian influenza viruses (AIVs) has been detected either in waterfowl, land-based poultry or in the environment in Bangladesh. AIV infections in Bangladesh affected a wide range of host species of terrestrial poultry. The highly pathogenic avian influenza (AI) H5N1 and low pathogenic AI H9N2 were found to co-circulate and be well entrenched in the poultry population, which has caused serious damage to the poultry industry since 2007. By reviewing the available scientific literature, the overall situation of AIVs in Bangladesh is discussed. All Bangladeshi (BD) H5N1 and H9N2 AIV sequences available at GenBank were downloaded along with other representative sequences to analyse the genetic diversity among the circulating AIVs in Bangladesh and to compare with the global situation. Three different H5N1 clades, 2.2. 2, 2.3. 2.1 and 2.3. 4.2, have been detected in Bangladesh. Only 2.3. 2.1a is still present. The BD LP H9N2 viruses mostly belonged to the H9 G1 lineage but segregated into many branches, and some of these shared internal genes with HP viruses of subtypes H7N3 and H5N1. However, these reassortment events might have taken place before introduction to Bangladesh. Currently, H9N2 viruses continue to evolve their HA cleavage, receptor binding and glycosylation sites. Multiple mutations in the HA gene associated with adaptation to mammalian hosts were also observed. Strict biosecurity at farms and gradual phasing out of live-bird markets could be the key measures to better control AIVs, whereas stamping out is not a practicable option in Bangladesh. Vaccination also could be an additional tool, which however, requires careful planning. Continuous monitoring of AIVs through systematic surveillance and genetic characterisation of the viruses remains a hallmark of AI control.
Topical rifampin powder for orthopedic trauma part I: Rifampin powder reduces recalcitrant infection in a delayed treatment musculoskeletal trauma model

Open fractures become infected despite meticulous debridement and care. Locally applied antibiotics, commonly embedded in polymethylmethacrylate, deliver high doses of drug directly to the fracture site. Direct application of antibiotic powder, which is being applied prophylactically in spine surgery, is a recent interest in the trauma sector, where bacterial biofilms are more prevalent. Traditional antibiotics, such as vancomycin, are poor performers against bacterial biofilms thus are ineffective in delayed treatment. Rifampin is an effective eradicator of Staphylococcal biofilms. Here, a rat model of musculoskeletal trauma was used to evaluate the utility of locally applied rifampin powder for reducing established orthopedic Staphylococcal infections in a delayed treatment scenario that previously indicated the limited use of local vancomycin. By applying rifampin powder directly to the contaminated segmental defect, the number of bacteria, as well as clinical indications of infection, were significantly reduced compared to vancomycin and daptomycin. Considering the Infectious Disease Society of America's recommendation to use rifampin in combination with another antibiotic to reduce the onset of rifampin resistance, rifampin powder was also applied in combination with vancomycin or daptomycin with insignificant changes in eradication performance. No indications of rifampin resistance were identified. Clinical Significance: The use of locally applied rifampin is a promising therapy for mature and tolerant musculoskeletal infections. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. J Orthop Res 36:3136–3141, 2018.
Social Class in a Mid-Eighteenth-Century Apulian Town: Indications from the Catasto Onciario

Cluster analysis is applied to the mid-eighteenth-century tax register and household census of the southern Italian town of Locorotondo in the Province of Bari in order to reconstruct aspects of social class. Other documentary sources such as notarial transactions are also brought to bear on the study. It is argued that in this zone there existed a degree of social mobility even within the strictures of late feudalism, that both an entrepreneurial elite and yeoman peasantry existed, and that analysts of synchronic documents of this kind must be careful about taking occupational categories as coterminous with social class categorizations. In this article I will discuss social class in the town of Locorotondo, Province of Bari, southern Italy, at the middle of the eighteenth century. I intend it both as a substantive contribution to our knowledge of southern Italian peasant culture in its historical dimension and as a demonstration of methodologies which can be applied to a set of documents which have been little utilized by anthropologists. Recently anthropologists working in Italy have turned their attention to historical problems and historical methodologies (Blok 1974; Douglass 1980 and 1984; Kertzer 1984; Schneider and Schneider 1976). Similarly historians have used anthropological understandings in reconstructing aspects of Italian society in the past (Bell I979; Herlihy and Klapisch-Zuber I985). This article is informed by such interdisciplinary approaches and is part of a continuing project meant to produce an anthropological history of Locorotondo which traces the formation of the unique peasant cultural patterns of the zone, the Murgia dei Trulli, in which it is located. The murgia, or plateau, is characterized by two things which set it apart from other areas in rural south Italy. First are the trulli themselves. These coneroofed peasant dwellings are found only in this area of Italy and are widely known from travel posters and picture books. Second, in contrast to the more Ethnohistory 33:4 (Fall 1986). Copyright ? by the American Society for Ethnohistory. ccc ooI4-I8oI/86/$I.5o. This content downloaded from 157.55. 39.104 on Mon, 20 Jun 2016 06:06:07 UTC All use subject to http://about.jstor. org/terms