Miracle-dz/UniFAR-FTUs huggingface dataset:
Practice patterns of diabetic retinopathy referral among doctors in a tertiary hospital

Background: There were 31.7 million diabetics in India in year 2000 with a projection to reach 79.4 million by year 2030. We must identify and treat high-risk persons before severe loss of vision occurs. We doctors of all specialities have to strive together to create awareness of the importance of routine eye evaluation for all diabetics as this blindness is largely irreversible once set in. Visual impairment as a result of Diabetic Retinopathy (DR) has a significant impact on patients’ quality of life. In communities in which intensive retinopathy screening programmes have been implemented, rates of vision loss have decreased. There is a need to increase the awareness among doctors of all specialities on the importance of retinal examination by ophthalmologists even in well controlled diabetics. Aims & Objective: A survey to assess the practice patterns among doctors about diabetic retinopathy referral, its complications, treatment modalities and the knowledge about timing of referral to ophthalmologists. Material and Methods: Questionnaires consisting of 16 questions pertaining to general awareness, clinical manifestations, complications and treatment was given to doctors in two sections A and B. Answers were analysed and tabulated. Results: 36 doctors of various specialities participated in the survey. 19.4% of doctors felt there was no need to refer all diabetics routinely for fundus examination. 80.6% (29 of 36) of doctors were regularly referring all diabetics to ophthalmologist, where as 19% did not. 86.1% of the participants felt there was no need to worry about retinopathy if blood sugar levels were controlled. Amongst the participants 75% were well aware of DR, its presentation, complications and 88.9% about its treatment. Conclusion: Diabetic retinopathy still is not well understood among general doctors and non-ophthalmologists. It is therefore advisable to educate consultants about the severity of the problem and need for early referral to prevent complications. General Practitioners can be educated about the timing to seek expert opinion for treatment.
Cambios del segmento anterior medidos con Pentacam, después de iridotomías con YAG en pacientes con ángulo estrecho

Objetivo: Medir con Pentacam los cambios del segmento anterior en ojos con camara anterior y angulo clinicamente estrechos, a los cuales se les realizaron iridotomias con laser de Yag. Diseno: Descriptivo, prospectivo, longitudinal. Pacientes: Se incluyeron 13 pacientes (26 ojos) detectados con angulo estrecho, los cuales eran clinicamente candidatos a iridotomias con laser de Yag. Metodo: En todos los pacientes se realizo estudio de Pentacam antes y un mes despues de iridotomias con laser de Yag. Mediciones mas importantes: Profundidad de la camara anterior en el centro y media periferia, volumen de la camara anterior y amplitud del angulo. Resultados: Se estudiaron 26 ojos de 13 pacientes, todas ellas mujeres, con promedio de edad de 65.08 anos. La profundidad central de la camara anterior preoperatoria fue de 2.28 ± 0.33 mm y postoperatoria de 2.31 ± 0.35 mm (p = 0.008). La profundidad de la camara anterior en la media periferia superior preoperatoria fue de 1.31 ± 0.27 mm y postoperatoria de 1.45 ± 0.21 mm (p = 0.000). La profundidad de la camara anterior en la media periferia inferior preoperatoria fue de 1.55 ± 0.26 mm y postoperatoria de 1.70 ± 0.23 mm (p = 0.000). La profundidad de la camara anterior en la media periferia nasal preoperatoria fue de 1.38 ± 0.29 mm y postoperatoria de 1.46 ± 0.21 mm (p = 0.003). La profundidad de la camara anterior en la media periferia temporal preoperatoria fue de 1.53 ± 0.24 mm y postoperatoria de 1.73 ± 0.26 mm (p = 0.000). El volumen de la camara anterior preoperatorio fue de 100.81 ± 16.93 mm3 y postoperatorio de 122.42 ± 18.89 mm3 (p = 0.000). El promedio del angulo preoperatorio fue de 26.63± 5.97R y postoperatorio de 27.40 ± 5.12R (p = 0.044). No hubo diferencia estadisticamente significativa en el diametro pupilar pre y postoperatorio. El grosor corneal, y las queratometrias no se modificaron. Conclusiones: Este estudio demuestra de manera cuantitativa que los cambios en la profundidad y volumen de la camara anterior y en la amplitud del angulo son estadisticamente significativos despues de iridotomias con laser de Yag en pacientes con angulo estrecho. Palabras clave: Iridotomia, Nd: Yag laser, angulo estrecho, Pentacam.
Homeostatic mechanisms regulate distinct aspects of cortical circuit dynamics

Significance Despite decades of intense studies on homeostasis, network properties undergoing homeostatic regulation remain elusive. Furthermore, whether diverse forms of homeostatic plasticity are simply redundant or serve distinct functions is unclear. Here, our data show that functional correlations are subject to homeostatic regulation, both in terms of average amplitude and their structure. A computational model demonstrates that synaptic scaling is essential for the restoration of correlations and network structure, whereas intrinsic plasticity is crucial for the recovery of firing rates after perturbations, suggesting that synaptic scaling and intrinsic plasticity distinctly contribute to homeostatic regulation. Homeostasis is indispensable to counteract the destabilizing effects of Hebbian plasticity. Although it is commonly assumed that homeostasis modulates synaptic strength, membrane excitability, and firing rates, its role at the neural circuit and network level is unknown. Here, we identify changes in higher-order network properties of freely behaving rodents during prolonged visual deprivation. Strikingly, our data reveal that functional pairwise correlations and their structure are subject to homeostatic regulation. Using a computational model, we demonstrate that the interplay of different plasticity and homeostatic mechanisms can capture the initial drop and delayed recovery of firing rates and correlations observed experimentally. Moreover, our model indicates that synaptic scaling is crucial for the recovery of correlations and network structure, while intrinsic plasticity is essential for the rebound of firing rates, suggesting that synaptic scaling and intrinsic plasticity can serve distinct functions in homeostatically regulating network dynamics.
KARAKTERISASI DAN SKRINING FITOKIMIA SIMPLISIA BUAH SELUTUI PUKA (Tabernaemontana macracarpa Jack)

Selutui puka (Tabernaemontana macrocarpa Jack) is a plant that is efficacious for treating tumor diseases and blisters. Simplicia is said to be of high quality if it meets the simplicia requirements. The initial process to find out the quality of simplicia is characterization. The study aims to determine the specific, non-specific characteristics and content of chemical compounds.This research is non experimental. The research starts from sampling, determination, making simplicia, characterization which includes macroscopic test, microscopic test, determination of moisture content, soluble ethanol extract content, water soluble extract content, moisture content, ash content, acid insoluble ash content and phytochemical screening. Data were analyzed using descriptive methods.Specific characteristics in the macroscopic and organoleptic tests showed long round leaves, pinnate leaf bones, spiky rounded leaf tips, rounded base of leaves, flat leaf edges, thick leaf flesh, dark green color, leaf width of 4.5 cm long, 12.5 cm long. The powder is dark green, aromatic and has a bitter taste. Microscopic tests include cover hair, vessels, bundles of stairs, upper epidermis and lower epidermis with bidiastic type stomata, 12% soluble ethanol, 15% water soluble extract. Non-specific characteristics consisted of 8% moisture content, 6.51% ash content, acid insoluble ash content 0.246%. The results of phytochemical screening contain alkoloid, flavonoids, tannins, saponins and steroids.
Characterising the influence of different wheat cultivar rhizospheres on variations in microbiome diversity and functionality

In agricultural systems plant diseases caused by soil borne fungi are regarded as the most devastating. Wheat is recognized as an important crop worldwide, but it is highly susceptible to Take-all disease caused by the soil ascomycete fungus Gaeumannomyces graminis var. tritici (Ggt). Interest in biological control of Take-all has increased due to a lack of resistant wheat cultivars and chemical pesticides. Although this disease has been extensively studied it is still regarded as an excellent model for biological control of plant root diseases. Pseudomonas bacteria in the P. fluorescens complex are well recognized for their plant growth promoting and disease suppressive properties and they can often be found to be prevalent in controlling Take all. In this work Pseudomonas isolates from the rhizosphere and endosphere of two wheat varieties, Hereward High Take-all Build up (H-TAB) and Cadenza Low Take-all Build up (L-TAB) were investigated. These isolates were screened for the presence or absence of two rhizosphere fitness loci, wsm and fecB, involved in host recognition and iron acquisition, respectively. It was found that these loci were significantly differentially associated with the two wheat cultivars where wsm was more abundant within the Hereward isolates while the fecB was found more within the Cadenza isolates. In addition, these isolates were tested for their in vitro inhibition of Ggt, which led to the identification of six strong Ggt growth inhibition isolates. Furthermore, testing these antagonistic isolates in the presence of the plant revealed that isolate 25R-7 was able to reduce the number of infected roots on Cadenza, while isolate 30R-11 reduced the number of infected roots on Hereward. Overall, the mixture of the six strong isolates reduced the number of infected roots in both cultivars more than that of individual strains. In addition the structure of bacterial communities associated with five wheat varieties (two L-TAB and three H-TAB) along with one barley (Unknown iii TAB) grown continually at the same site in three fields for a period of 5 years were investigated. The main difference in the structure of bacterial communities was based on field type and the rhizosphere samples separated well from those of bulk soil. Overall, no significant differences were found between the cultivars over time. The soil DNA concentrations of Ggt along with the soil DNA concentrations of bacteria, Pseudomonas and fungi were also studied from the same treatments. Year-to-year variation was the major factor in determining the amount of bacterial, Pseudomonas, fungal and Ggt DNA in the three fields.
Vancomycin-Resistant Enterococcal iters Diminish Among Patients With Recurrent Clostridium difficile Infection After Administration of SER-109, A Novel Microbiome Agent

Background Mary-Jane Lombardo, PhD1, Marin Vulic, PhD1, Toshi Ohsumi, PhD1, David Cook, PhD1, Matthew Henn, PhD1, Colleen Kraft, MD2, Sahil Khanna, MBBS, MS3, Darrell Pardi, MD, MS3 and Elizabeth Hohmann, MD, FIDSA4 (1)Seres Therapeutics, Inc, Cambridge, MA, (2)Emory University School of Medicine, Atlanta, GA, (3)Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, (4)Infectious Diseases, Massachusetts General Hospital, Boston, MA Vancomycin-resistant enterococcal (VRE) titers diminish among patients with recurrent Clostridium difficile infection after administration of SER-109, a novel microbiome agent
Nutrition of goats, sheep and cattle in tropical and warm conditions « Evaluation of energy and protein requirements and animal responses to diet. Evaluation of INRA system to predict nutritive value of forage resources »

The overall aim of the thesis project was to generate knowledge to contribute to the development of good feeding practices for sheep goats and cattle in warm regions. The methodology used in this project crossed meta-analysis to an experimental approach. The maintenance energy requirements of goats, sheep and cattle in warm regions are higher than those of ruminants in temperate regions. These differences were partly attributed to the capacity of livestock genotypes of these regions to mobilize a fraction of the nutrients ingested for unproductive functions adaptation to stress and the energy cost of ingestion and digestion of more fibrous diets. The estimation for the energy requirements for production was the same order of magnitude as the genotypes of temperate regions. Our estimates of protein requirements for maintenance and production show that they are higher with tropical genotypes compared to temperate genotypes.The hierarchy of needs between species varies with their modes of expression (expression of metabolic weight). The energy and protein supply unit system of INRA, based on a mechanistic approach to the use of feed, potentially leads to a good assessment of food resources. However, some factors must be revised to reflect the specific composition of forage resources in warm regions.
Genetic assignment of individuals to source populations using network estimation tools

Dispersal, the movement of individuals between populations, is crucial in many ecological and genetic processes. However, direct identification of dispersing individuals is difficult or impossible in natural populations. By using genetic assignment methods, individuals with unknown genetic origin can be assigned to source populations. This knowledge is necessary in studying many key questions in ecology, evolution and conservation. We introduce a network‐based tool BONE (Baseline Oriented Network Estimation) for genetic population assignment, which borrows concepts from undirected graph inference. In particular, we use sparse multinomial Least Absolute Shrinkage and Selection Operator (LASSO) regression to estimate probability of the origin of all mixture individuals and their mixture proportions without tedious selection of the LASSO tuning parameter. We compare BONE with three genetic assignment methods implemented in R packages radmixture, assignPOP and RUBIAS. Probability of the origin and mixture proportion estimates of both simulated and real data (an insular house sparrow metapopulation and Chinook salmon populations) given by BONE are competitive or superior compared to other assignment methods. Our examples illustrate how the network estimation method adapts to population assignment, combining the efficiency and attractive properties of sparse network representation and model selection properties of the L1 regularization. As far as we know, this is the first approach showing how one can use network tools for genetic identification of individuals' source populations. BONE is aimed at any researcher performing genetic assignment and trying to infer the genetic population structure. Compared to other methods, our approach also identifies outlying mixture individuals that could originate outside of the baseline populations. BONE is a freely available R package under the GPL licence and can be downloaded at GitHub. In addition to the R package, a tutorial for BONE is available at https://github.com/markkukuismin/BONE/.
Fermented Cereal Gruels: Towards a Solution of the Weanling's Dilemma

The high incidence of diarrhoeal morbidity a the onset of weaning is due in part to consumption of contaminated food. This paper discusses the possible role of fermentation as a household food preparation technology in the improvement of the microbial quality of weaning foods as well as in providing adequate nutrients for infant growth and development. It discusses the extent to which fermented foods provide adequate nutrients; the degree to which fermentation can reduce the levels of aflatoxins, hydrocyanic acid, and other toxins in foods; whether fermentation reduces contamination of weaning foods by pathogens; and the role of fermented foods in reducing diarrhoeal morbidity, severity, and duration.
Role of general regulatory factors in the control of gene expression and transcription fidelity

The last decades have been marked by the discovery of pervasive transcription. Indeed, many studies have shown that transcription by RNA polymerase II is not restricted to annotated regions but is widespread in eukaryotic genomes, leading to the production of a plethora of non-coding RNAs. Precise delimitation of transcriptional units appears to be essential to ensure robust fidelity of gene expression and to maintain the integrity of DNA-associated events by preventing the occurrence of conflicts with transcription. In this respect, accurate transcription initiation and termination represent crucial mechanisms to partition the genome and define the correct processing of RNA molecules. Here, we show that yeast general regulatory factors (GRFs), a class of highly expressed transcription regulators, control pervasive transcription at the level of initiation and termination and are also involved in the fidelity of initiation of mRNA-coding genes. We demonstrate that GRFs bound at promoter regions can elicit transcription termination by physically impeding the progression of polymerases mainly deriving from readthrough transcription at upstream canonical termination sites. We provide evidence that this termination pathway named roadblock is widespread throughout the yeast genome and protects promoter regions from transcriptional interference. Furthermore, we establish that the presence of general regulatory factors also limits pervasive transcription at the level of initiation, notably by occluding spurious transcription start sites present in the vicinity of their binding sites. We also unveil the importance of these factors in promoting correct transcription start site selection at mRNA-coding genes thus favouring the synthesis of transcripts with an appropriate coding potential. Finally, we determine that the role of GRFs in controlling proper initiation is intimately linked to their ability to correctly position nucleosomes in promoters, a role that occurs independently from but in cooperation with chromatin remodelers.
Experimental evolution of plasmid genomes

The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. The multi-copy state of plasmids leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. Consequently, I hypothesize that genetic drift of plasmid alleles during cell division has implication for the evolutionary rates of plasmids by lowering the number of accumulating mutations that are expected from the mutational supply. To test this hypothesis, I performed an experimental evolution experiment of low- and high-copy non-mobile plasmids in an Escherichia coli host. The results of the experiment revealed that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. The results further suggest that many plasmid mutations are quickly lost due to genetic drift during cell division. Here I term this special type of allele dynamics in the population as ‘segregational drift’. Thus, segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. In conclusion, depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. Plasmid copy number is thus an important determinant of plasmid evolvability due to the manifestation of segregational drift.
Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales

Abstract The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within‐host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.
Reprogramming of spermatogonial stem cells into pluripotent stem cells in the spheroidal state

ABSTRACT Spermatogonial stem cells (SSCs) are unipotent adult stem cells, capable of differentiating into sperm cells. SSCs can be cultured in vitro for a long time. SSCs expressing Oct4, a pluripotency marker, and are the only adult cells which pluripotency can be induced under defined culture conditions. However, because 2D culture imposes limitations in cell junction formation, cell shape, metabolism, response to stimuli, and cell interface with medium, mechanistic studies on reprogramming of SSCs using feeder cells still have many challenges. Recent studies have shown that a culture system using a bio-matrix can be used in long-term feeder-free SSCs culture and for induction of pluripotency in SSCs. However, the bio-matrix cannot be the optimal micro-environment in mechanistic studies because it creates a physical barrier to growth factors and other signaling molecules. To overcome this effect of the matrix, we reprogrammed SSCs into pluripotent ESC-like cells, so-called germline-derived pluripotent stem cells (gPSCs) by using a 3D scaffold, in which cells are less responsive to external stimuli than in 2D cultures. Thus, we confirm the possibility of SSC reprogramming in the spheroidal state and suggest the utility of 3D scaffolds as a tool for studying the mechanism of SSC reprogramming into gPSCs without a bio-matrix.