Miracle-dz/UniFAR-FTUs huggingface dataset:
Puzzling Out the Genetic Architecture of Endometriosis: Whole-Exome Sequencing and Novel Candidate Gene Identification in a Deeply Clinically Characterised Cohort

Endometriosis (EM) is a common multifactorial gynaecological disorder. Although Genome-Wide Association Studies have largely been employed, the current knowledge of the genetic mechanisms underlying EM is far from complete, and other approaches are needed. To this purpose, whole-exome sequencing (WES) was performed on a deeply characterised cohort of 80 EM patients aimed at the identification of rare and damaging variants within 46 EM-associated genes and novel candidates. WES analysis detected 63 rare, predicted, and damaging heterozygous variants within 24 genes in 63% of the EM patients. In particular, (1) a total of 43% of patients carried variants within 13 recurrent genes (FCRL3, LAMA5, SYNE1, SYNE2, GREB1, MAP3K4, C3, MMP3, MMP9, TYK2, VEGFA, VEZT, RHOJ); (2) a total of 8.8% carried private variants within eight genes (KAZN, IL18, WT1, CYP19A1, IL1A, IL2RB, LILRB2, ZNF366); (3) a total of 24% carried variants within three novel candidates (ABCA13, NEB, CSMD1). Finally, to deepen the polygenic architecture of EM, a comprehensive evaluation of the analysed genes was performed, revealing a higher burden (p < 0.05) of genes harbouring rare and damaging variants in the EM patients than in the controls. These results highlight new insights into EM genetics, allowing for the definition of novel genotype–phenotype correlations, thereby contributing, in a long-term perspective, to the development of personalised care for EM patients.
Estimation of Reference Evapotranspiration using the FAO Penman-Monteith Method for Climatic Conditions of Poland

Evapotranspiration is the combination of soil evaporation and crop transpiration. Weather parameters, crop characteristics, management and environmental factors affect evapotranspiration. Reference, potential and actual evapotranspiration are distinguished. These terms are commonly used, although some differences of their definitions can be found among researches. The potential evapotranspiration of a given crop is defined as soil evaporation and plant transpiration under unlimited soil water supply and actual meteorological conditions. According to Brutseart (1982) the potential evapotranspiration is a maximum intensity of evapotranspiration from a large surface covered completely and homogeneously with actively growing plants under conditions of unlimited availability of soil water. Allen et al. (1998) call it the crop evapotranspiration under standard conditions and define as the evapotranspiration from disease-free, well-fertilized crops, grown in large fields, under optimum soil water conditions and achieving full production under the given climatic conditions. The actual evapotranspiration is the amount of water transpired from plants and evaporated from soil surface under actual meteorological conditions and under non-optimal soil, biological, management and environmental conditions. It differs from the potential evapotranspiration due to soil water shortage or waterlogging, diseases, soil salinity, low soil fertility. According to Allen et al. (1998) the evapotranspiration from crops grown under management and environmental conditions that differ from the standard conditions defined for the potential evapotranspiration can be called the crop evapotranspiration under nonstandard conditions. The evapotranspiration from a reference surface is called the reference evapotranspiration and is denoted as ETo. A large uniform grass (or alfalfa) field is considered worldwide as the reference surface. The reference grass crop completely covers the soil, is kept short, well watered and is actively growing under optimal agronomic conditions. Reference evapotranspiration (ETo) is an important agrometeorological parameter for climatological and hydrological studies, as well as for irrigation planning and management. There are several methods to estimate ETo. The FAO Penman-Monteith (FAO PM) method has been considered as a universal standard to estimate ETo (Allen et al., 1989, 1994, 1998;
Geovisualization Using HTML5 : a case study to improve animations of historical geographic data

Popular science Visualize geographic data Using HTML5 The Scanian Economic-Demographic Database (SEDD) has been assembled by the Centre for Economic Demography (CED), Lund University. It contains demographic and economic information of Scania from the 17th century until the present. The SEDD database has been integrated with geographic data, which are digitized from four independent historical maps. To help the users well understand these data, a web mapping application called SEDD Map has been developed and tested. The previous version of SEDD Map is constructed using Silverlight plugin. It cannot run on most popular portable devices. As Hypertext Markup Languages (HTML) continue to develop, a recent version, HTML5, was published in 2012. It aims to support the latest multimedia formats and reduce the need for plugins. So, to improve the compatibility of SEDD Map, this work using HTML5 to developed a new version of SEDD Map. Before we constructed the new version of SEDD Map, a set of web mapping applications and programs were evaluated. From this evaluation and comparison, we found that SEDD Map could be improved in many area, such as improving the animation of historical geographic data. Animation is a useful tool when presenting historical data. The geographic data in SEDD Map are taken from four independent historical maps. To visualize geographic data as an animation, we need to create a time sense sequential dataset. In this study, we used linear interpolation and the four historical maps as start years and end years to simulate 159 maps to visualize the geographic data as animations. From this study, we found that: The commonly used web mapping applications for investigating demographic data contain functions, such as interactive visualization, statistical graphics, basic map tools, animations, etc; HTML5 can replace (and improve) the used of Silverlight for web mapping; Animations can be generated (filling in what is missing is to improve the data sets).
Delays between the onset of symptoms and first rheumatology consultation in patients with rheumatoid arthritis in the UK: an observational study

Objective To investigate delays from symptom onset to rheumatology assessment for patients with a new onset of rheumatoid arthritis (RA) or unclassified arthritis. Methods Newly presenting adults with either RA or unclassified arthritis were recruited from rheumatology clinics. Data on the length of time between symptom onset and first seeing a GP (patient delay), between first seeing a general practitioner (GP) and being referred to a rheumatologist (general practitioner delay) and being seen by a rheumatologist following referral (hospital delay) were captured. Results 822 patients participated (563 female, mean age 55 years). The median time between symptom onset and seeing a rheumatologist was 27.2 weeks (IQR 14.1–66 weeks); only 20% of patients were seen within the first 3 months following symptom onset. The median patient delay was 5.4 weeks (IQR 1.4–26.3 weeks). Patients who purchased over-the-counter medications or used ice/heat packs took longer to seek help than those who did not. In addition, those with a palindromic or an insidious symptom onset delayed for longer than those with a non-palindromic or acute onset. The median general practitioner delay was 6.9 weeks (IQR 2.3–20.3 weeks). Patients made a mean of 4 GP visits before being referred. The median hospital delay was 4.7 weeks (IQR 2.9–7.5 weeks). Conclusion This study identified delays at all levels in the pathway towards assessment by a rheumatologist. However, delays in primary care were particularly long. Patient delay was driven by the nature of symptom onset. Complex multi-faceted interventions to promote rapid help seeking and to facilitate prompt onward referral from primary care should be developed.
Prognostic genes of breast cancer revealed by gene co-expression network analysis

The aim of the present study was to identify genes that may serve as markers for breast cancer prognosis by constructing a gene co-expression network and mining modules associated with survival. Two gene expression datasets of breast cancer were downloaded from ArrayExpress and genes from these datasets with a coefficient of variation >0.5 were selected and underwent functional enrichment analysis with the Database for Annotation, Visualization and Integration Discovery. Gene co-expression networks were constructed with the WGCNA package in R. Modules were identified from the network via cluster analysis. Cox regression was conducted to analyze survival rates. A total of 2,669 genes were selected, and functional enrichment analysis of them revealed that they were mainly associated with the immune response, cell proliferation, cell differentiation and cell adhesion. Seven modules were identified from the gene co-expression network, one of which was found to be significantly associated with patient survival time. Expression status of 144 genes from this module was used to cluster patient samples into two groups, with a significant difference in survival time revealed between these groups. These genes were involved in the cell cycle and tumor protein p53 signaling pathway. The top 10 hub genes were identified in the module. The findings of the present study could advance the understanding of the molecular pathogenesis of breast cancer.
PALE‐GREEN LEAF 1, a rice cpSRP54 protein, is essential for the assembly of the PSI‐LHCI supercomplex

Abstract Although photosynthetic multiprotein complexes have received major attention, our knowledge about the assembly of these proteins into functional complexes in plants is still limited. In the present study, we have identified a chlorophyll‐deficient mutant, pale‐green leaf 1 (pgl1), in rice that displays abnormally developed chloroplasts. Map‐based cloning of this gene revealed that OsPGL1 encodes a chloroplast targeted protein homologous to the 54‐kDa subunit of the signal recognition particle (cpSRP54). Immunoblot analysis revealed that the accumulation of the PSI core proteins PsaA and PsaB, subunits from the ATP synthase, cytochrome, and light‐harvesting complex (LHC) is dramatically reduced in pgl1. Blue native gel analysis of thylakoid membrane proteins showed the existence of an extra band in the pgl1 mutant, which located between the dimeric PSII/PSI‐LHCI and the monomeric PSII. Immunodetection after 2D separation indicated that the extra band consists of the proteins from the PSI core complex. Measurements of chlorophyll fluorescence at 77 K further confirmed that PSI, rather than PSII, was primarily impaired in the pgl1 mutant. These results suggest that OsPGL1 might act as a molecular chaperone that is required for the efficient assembly and specific integration of the peripheral LHCI proteins into the PSI core complex in rice.
Morphostructural evolution of active margin basins: the example of the Hawke Bay forearc basin, New Zealand.

The evolution of sedimentary basins depends on several factors that are erosion, transport and deposition. These factors are controlled by deformation (internal parameter), climate and eustasy (external parameters). The role of tectonic deformation is emphasized in active subduction margins. In addition, the significant Pleistocene climate and eustasy variations deeply influenced the stratigraphic architecture by tuning erosion, transport and deposition. The Hawke’s Bay forearc basin of the Hikurangi subduction margin in New Zealand is an exceptionally well preserved, exposed and investigated Pleistocene active forearc basin. The interpretation of a dense grid of both marine and onshore seismic data coupled with inland investigations of Pleistocene formations and core sampling led to the determination of (i) the detailed stratigraphy with the dominance of 40-100 Ka sequences, (ii) the geometry of these depositional sequences, that reveals the impact of tectonic deformation and (iii) the paleoenvironmental evolution for the last 1 Ma. We can propose a scenario for the Hawke’s Bay active forearc basin morphostructural evolution and discuss the impact of internal and external parameters in the acquisition of this morpho-structure.
Novel Freshwater Cyanophages Provide New Insights into Evolutionary Relationships between Freshwater and Marine Cyanophages

This study expands the current knowledge on freshwater cyanophage isolates and cyanophage genetic diversity, indicating that freshwater and marine cyanophages infecting Synechococcus spp. may share close genetic similarity and evolutionary relationships. ABSTRACT Cyanobacteria and cyanophages are present widely in both freshwater and marine environments. However, freshwater cyanophages remain unknown largely due to the small numbers of cyanophage isolates despite their ecological and environmental significance. In this study, we present the characterization of two novel lytic freshwater cyanophages isolated from a tropical inland lake in Singapore, namely, cyanopodovirus S-SRP01 and cyanomyovirus S-SRM01, infecting two different strains of Synechococcus spp. Functional annotation of S-SRP01 and S-SRM01 genomes revealed a high degree of homology with marine cyanophages. Phylogenetic trees of concatenated genes and whole-genome alignment provided further evidence that S-SRP01 is close evolutionarily to marine cyanopodoviruses, while S-SRM01 is evolutionarily close to marine cyanomyoviruses. Few genetic similarities between freshwater and marine cyanophages have been identified in previous studies. The isolation of S-SRP01 and S-SRM01 expand current knowledge on freshwater cyanophages infecting Synechococcus spp. Their high degree of gene sharing provides new insights into the evolutionary relationships between freshwater and marine cyanophages. This relatedness is further supported by the discovery of similar phenomenon from other freshwater viral metagenomes. IMPORTANCE This study expands the current knowledge on freshwater cyanophage isolates and cyanophage genetic diversity, indicating that freshwater and marine cyanophages infecting Synechococcus spp. may share close genetic similarity and evolutionary relationships.
The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study, and mitigating tools

Objective Applying the science of networks to quantify the discriminatory impact of the ICD-9-CM to ICD-10-CM transition between clinical specialties. Materials and Methods Datasets were the Center for Medicaid and Medicare Services ICD-9-CM to ICD-10-CM mapping files, general equivalence mappings, and statewide Medicaid emergency department billing. Diagnoses were represented as nodes and their mappings as directional relationships. The complex network was synthesized as an aggregate of simpler motifs and tabulation per clinical specialty. Results We identified five mapping motif categories: identity, class-to-subclass, subclass-to-class, convoluted, and no mapping. Convoluted mappings indicate that multiple ICD-9-CM and ICD-10-CM codes share complex, entangled, and non-reciprocal mappings. The proportions of convoluted diagnoses mappings (36% overall) range from 5% (hematology) to 60% (obstetrics and injuries). In a case study of 24 008 patient visits in 217 emergency departments, 27% of the costs are associated with convoluted diagnoses, with ‘abdominal pain’ and ‘gastroenteritis’ accounting for approximately 3.5%. Discussion Previous qualitative studies report that administrators and clinicians are likely to be challenged in understanding and managing their practice because of the ICD-10-CM transition. We substantiate the complexity of this transition with a thorough quantitative summary per clinical specialty, a case study, and the tools to apply this methodology easily to any clinical practice in the form of a web portal and analytic tables. Conclusions Post-transition, successful management of frequent diseases with convoluted mapping network patterns is critical. The http://lussierlab.org/transition-to-ICD10CM web portal provides insight in linking onerous diseases to the ICD-10 transition.
Creep and quakes on the northern transition zone of the San Andreas fault from GPS and InSAR data

The San Juan Bautista (SJB) segment forms the northern transition zone of the creeping section of the San Andreas fault. It is an area of moderate seismicity; the largest instrumentally‐recorded earthquakes have been M5.5. However, historic records suggest six M ≥ 6 earthquakes occurred near the SJB segment between 1840 and 1899. It is also an area that has experienced several slow earthquakes. We perform a joint inversion of GPS and InSAR data to determine the current rate and distribution of interseismic creep. We find two low‐slip/locked segments at mid‐seismogenic depths that may represent source regions for the 19th century earthquakes. We find that the SJB segment is currently accumulating strain energy at the rate of one M6.3–6.7 earthquake per century. At this rate, the 1840–1899 sequence released 135–510 years of accumulated moment deficit.
Environmental catastrophe in the Pacific Islands around A.D. 1300

Paleosea-level data for the Pacific Islands suggest that sea level in the region fell, possibly in two stages, between 680 and 475 cal yr B.P. (A.D. 1270–1475). This was associated with a ∼1.5°C fall in temperature (determined from oxygen-isotope analysis) and an observed increase in El Nino frequency. For a long time, it has been clear that these changes—characterized as the “A.D. 1300 event”—brought about environmental and cultural changes on Pacific Islands. These are documented here systematically for the first time. Temperature fall, sea-level fall, and possibly short-lived precipitation increase are the principal effects of the A.D. 1300 event. Temperature fall stressed ecosystems, but its effects are difficult to separate from those of the others. Sea-level fall saw dramatic falls of nearshore coral-reef productivity and the formation of (habitable) reef islands (motu). Precipitation rise increased upland erosion and lowland sedimentation. The human outcomes of these environmental changes are organized in three groups: conflict, settlement-pattern changes, and the end of long-distance voyaging. Conflict increased during/after the A.D. 1300 event because of an abrupt fall in the food resource base. This also caused large coastal settlements on many islands to be abandoned in favor of caves and/or smaller fortified hilltop settlements. Successful long-distance voyages ceased during/after the A.D. 1300 event, as did interisland exchange within many archipelagoes. The regional (rather than local) extent of the A.D. 1300 event is demonstrated. Questions remain as to its synchronicity and duration. © 2000 John Wiley & Sons, Inc.
Interannual Climate Variability over the Tropical Pacific Ocean Induced by the Indian Ocean Dipole through the Indonesian Throughflow

The authors' previous dynamical study has suggested a link between the Indian and Pacific Ocean interannual climate variations through the transport variations of the Indonesian Throughflow. In this study, the consistency of this oceanic channel link with observations is investigated using correlation analyses of observed ocean temperature, sea surface height, and surface wind data. The analyses show significant lag correlations between the sea surface temperature anomalies (SSTA) in the southeastern tropical Indian Ocean in fall and those in the eastern Pacific cold tongue in the following summer through fall seasons, suggesting potential predictability of ENSO events beyond the period of 1 yr. The dynamics of this teleconnection seem not through the atmospheric bridge, because the wind anomalies in the far western equatorial Pacific in fall have insignificant correlations with the cold tongue anomalies at time lags beyond one season. Correlation analyses between the sea surface height anomalies (SSHA) in the southeastern tropical Indian Ocean and those over the Indo-Pacific basin suggest eastward propagation of the upwelling anomalies from the Indian Ocean into the equatorial Pacific Ocean through the Indonesian Seas. Correlations in the subsurface temperature in the equatorial vertical section of the Pacific Ocean confirm the propagation. In spite of the limitation of the short time series of observations available, the study seems to suggest that the ocean channel connection between the two basins is important for the evolution and predictability of ENSO.
Detecting Disease Outbreaks in Mass Gatherings Using Internet Data

Background Mass gatherings, such as music festivals and religious events, pose a health care challenge because of the risk of transmission of communicable diseases. This is exacerbated by the fact that participants disperse soon after the gathering, potentially spreading disease within their communities. The dispersion of participants also poses a challenge for traditional surveillance methods. The ubiquitous use of the Internet may enable the detection of disease outbreaks through analysis of data generated by users during events and shortly thereafter. Objective The intent of the study was to develop algorithms that can alert to possible outbreaks of communicable diseases from Internet data, specifically Twitter and search engine queries. Methods We extracted all Twitter postings and queries made to the Bing search engine by users who repeatedly mentioned one of nine major music festivals held in the United Kingdom and one religious event (the Hajj in Mecca) during 2012, for a period of 30 days and after each festival. We analyzed these data using three methods, two of which compared words associated with disease symptoms before and after the time of the festival, and one that compared the frequency of these words with those of other users in the United Kingdom in the days following the festivals. Results The data comprised, on average, 7.5 million tweets made by 12,163 users, and 32,143 queries made by 1756 users from each festival. Our methods indicated the statistically significant appearance of a disease symptom in two of the nine festivals. For example, cough was detected at higher than expected levels following the Wakestock festival. Statistically significant agreement (chi-square test, P<.01) between methods and across data sources was found where a statistically significant symptom was detected. Anecdotal evidence suggests that symptoms detected are indeed indicative of a disease that some users attributed to being at the festival. Conclusions Our work shows the feasibility of creating a public health surveillance system for mass gatherings based on Internet data. The use of multiple data sources and analysis methods was found to be advantageous for rejecting false positives. Further studies are required in order to validate our findings with data from public health authorities.
The relationship of the lunar regolith less than 10 micrometer fraction and agglutinates. I - A model for agglutinate formation and some indirect supportive evidence

The first part of a study of the 'less than 10 micrometer' soil fraction and agglutinates is concerned with the chemical systematics of the considered fraction of lunar soils, taking into account a model for agglutinate formation based on the fusion of the finest fraction (FFF). Attention is given to some evidence which supports the FFF model. The evidence is based on some indirect approaches to an estimation of the composition of the fused soil component. It is found that the 'less than 10 micrometer' soil fraction from all Apollo sites except Apollo 16 (which can be explained) is more feldspathic and enriched in incompatible elements (e.g., K and Th) than the bulk soil. It is concluded that these systematics result from simple comminution in which feldspar breaks down to finer sizes than pyroxene and olivine and the fine-grained incompatible-element-enriched mesostasis concentrates in the 'less than 10 micrometer' soil fraction.