Miracle-dz/UniFAR-FTUs huggingface dataset:
PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases

The discovery of disease‐causing mutations typically requires confirmation of the variant or gene in multiple unrelated individuals, and a large number of rare genetic diseases remain unsolved due to difficulty identifying second families. To enable the secure sharing of case records by clinicians and rare disease scientists, we have developed the PhenomeCentral portal (https://phenomecentral.org). Each record includes a phenotypic description and relevant genetic information (exome or candidate genes). PhenomeCentral identifies similar patients in the database based on semantic similarity between clinical features, automatically prioritized genes from whole‐exome data, and candidate genes entered by the users, enabling both hypothesis‐free and hypothesis‐driven matchmaking. Users can then contact other submitters to follow up on promising matches. PhenomeCentral incorporates data for over 1,000 patients with rare genetic diseases, contributed by the FORGE and Care4Rare Canada projects, the US NIH Undiagnosed Diseases Program, the EU Neuromics and ANDDIrare projects, as well as numerous independent clinicians and scientists. Though the majority of these records have associated exome data, most lack a molecular diagnosis. PhenomeCentral has already been used to identify causative mutations for several patients, and its ability to find matching patients and diagnose these diseases will grow with each additional patient that is entered.
Remotely-sensed indicators of burning efficiency of savannah and forest fires

The objective of this study was to test remotely sensed indicators of burning efficiency for savanna and forest fires in Central Africa. The timing of fire with respect to vegetation senescence, the rate of post-fire recovery of vegetation and the spatial pattern of burning were potential indicators of burning efficiency. Statistical analyses were conducted to assess whether the values of a vegetation index (NDVI) and surface temperature ( T s ) were different at different stages of the burning season for burnt and unburnt areas, fragmented and continuous burnt patches, and early and late fires. Results show that fires affect areas with the lowest NDVI and highest T s values. Continuous and fragmented burnt patches are associated with vegetation covers in different states prior to a fire. The rate of recovery of vegetation after a fire depends on ecotypes (periforests recover more slowly than savannas), burning intensity and completeness (areas affected by fragmented burnt patches recover more quickly than areas affected by continuous burnt patches) and timing of the fire (areas affected by early fires recover more quickly than areas affected by late fires). The results suggest that combustion efficiency is lower for fragmented burnt areas compared to continuous burnt areas. It would thus be possible to decrease uncertainties in estimates of trace gas emissions from fires by replacing fixed burning efficiency values in emission models by values that would vary in space and time, based on measures of the spatial pattern of burnt areas as detected by remote sensing.
Effects of land-use change from grassland to forest on soil sulfur and arylsulfatase activity in New Zealand

The effects of land-use change from grassland to forest on soil sulfur (S) and arylsulfatase enzyme activity were investigated by comparing soils under unimproved grassland and an adjacent 19-year-old exotic forest stand (mixture of Pinus ponderosa and P. nigra). Results showed that concentrations of organic S in topsoil under forest were significantly lower [418 µg/g (0–5 cm), 398 µg/g (5–10 cm)] than corresponding soil depths under grassland [541 µg/g (0–5 cm), 468 µg/g (5–10 cm)]. On the other hand, inorganic S concentrations were significantly higher in soil under forest at all depths compared with grassland. The inorganic S concentration in soil under grassland increased with depth, but there was no significant difference observed at different depths under forest. The decrease in organic S [and organic carbon (C)] in soil under forest was due to the enhanced mineralisation of organic components. The accumulation of inorganic S in the soil profile under forest was mainly attributed to enhanced mineralisation, although decreased leaching, increased sulfate-S adsorption, and increased atmospheric inputs by canopy interception of aerosols could have contributed. Microbial biomass C and S and arylsulfatase activity were higher in topsoil under grassland than forest. Lower arylsulfatase activities under forest compared with grassland at the time of sampling suggest that mineralisation of organic S under forest was not currently mediated primarily by enzyme activity, although enzyme activity may have been important at earlier stages of forest development. Arylsulfatase activity was significantly correlated with soil organic C, water-soluble C, microbial biomass C, total S, organic S, and microbial biomass S in soil under grassland and forest. Significant concentrations of organic S and microbial biomass S were present in the forest floor (litter and fermentation layers). These pools would be important for S cycling and availability in forest ecosystems. S mineralisation, S fractions, microbial biomass S, microbial biomass C.
Security analysis of OpenDaylight, ONOS, Rosemary and Ryu SDN controllers

There is an immense expectation on Software-Defined Networking (SDN) in industry as a novel approach towards potentially replacing conventional network management and control. However, SDN is not immune to security vulnerabilities which currently exist in the legacy systems or which may newly arise due to change in the network design. Since the beginning of SDN development, primary focus of research was on separation of control plane from data plane by keeping performance and operational flexibility unchanged. In the due course of achieving this, security aspects of an SDN have taken a back seat. Even though separation of control plane from a data plane is a great step towards simplification of network management, it subjects the network into a potential two way target for intruders to gain control. Due to the centralized design of SDN, compromising security of a controller will be as good as compromising the security of a whole network. Enterprises which are moving towards adapting SDN are concerned about security issues and the resulting problems. In this paper, we analyze the security issues of few of the widely used controllers. We found that the OpenDaylight controller is the most secure one compared to the other controllers. In addition, this paper also provides a snapshot of current development in security aspect of SDN controllers such that it may help SDN controller developers to identify the issues and rectify the same in future releases.
Radiocarbon in the Arabian Sea water column: Temporal variations in bomb 14C inventory since the GEOSECS and CO2 air‐sea exchange rates

Results of measurements of 14C in the upper 1500 m water column in 10 stations of the Arabian Sea are presented. The study carried out during 1994–1995, which includes reoccupation of three Geochemical Ocean Sections Study (GEOSECS) stations (1977–1978), provides an opportunity to assess the temporal variations in the distribution and inventory of bomb radiocarbon over a period of ∼2 decades. The Δ14C values of surface waters (5 m) range between 31 and 58‰, ∼20‰ less than those measured during 1978 at the three GEOSECS stations. The higher Δ14C values measured during the present (as well as GEOSECS) study occur in the southern Arabian Sea, which can be attributed to the influx of low-salinity and high-Δ14C waters from the Bay of Bengal. The Δ14C in the Persian Gulf Water (PGW) and the Red Sea Water (RSW) are in the range of −34 to −59‰ and −89 to −113‰, respectively, and do not show any significant differences from those measured during the GEOSECS. The bomb 14C inventories at the three GEOSECS stations during 1977 and 1995 show that at station 417 in the central Arabian Sea it has increased by ∼30%, whereas at the other two stations, 416 and 418 in the north and south central Arabian Sea, it is nearly the same. In general, the bomb 14C inventory in the region ranges between 3.5 and 7.7×109 atoms cm−2. The CO2 air-sea exchange rates, derived from the bomb 14C inventory, yield values of 7–16 mol m−2 yr−1. These exchange rates coupled with reported pCO2 measurements in surface Arabian Sea waters yield CO2 evasion rates in the range of 50–180 Tg-C yr−1 for the Arabian Sea.
Crime, Poverty and Police Corruption in Developing Countries

Crime and the fear of being hit by crime and small-scale violence are key economic and social problems in most developing countries, not least felt strongly by the poor. Extensive corruption in the police, experienced or perceived, contributes seriously to the problem. A key question raised in the paper is: How is police corruption linked to the wider processes of development - including crime, violence and poverty? The paper examines (i) how and why corruption may arise in the daily routines of the police and whether it may have impacts on crime rates; (ii) empirical indications of whether the police may be more corrupt than other groups of public officials; (iii) how and why police corruption may vary across countries; and (iv) the wider impacts of police corruption on development
An evaluation of snowline data across New Guinea during the last major glaciation , and area-based glacier snowlines in the Mt . Jaya region of Papua , Indonesia , during the Last Glacial Maximum

Geomorphological mapping and lake-core data from Mt. Jaya, western New Guinea, show that Last Glacial Maximum (LGM) glaciation was less extensive than previously thought. Average equilibrium line altitudes (ELAs), calculated using the area–altitude-balance ratio method, for minimum and maximum ice configurations were 4050749 and 4000756m a.s. l. , respectively. This is about 600m below the ELA of the Mt. Jaya glaciers in 1971–73 and ca 400m higher than values previously quoted for LGM ELAs in this area. A reappraisal of the evidence used to reconstruct the ELA of glaciers across New Guinea suggests that published chronologies are not sufficient to demonstrate that reported ELAs fall within the LGM window of 21,00072 yr BP. Furthermore, the published information only constrains the altitude of the ELAs between 3400 and 3800m a.s. l. , not including uncertainty in topography. A simple mass and energy-balance model indicates that an ELA depression of 500m (i.e., the observed change at Mt. Jaya after adjustment for sea-level change) could be accomplished with 2.5–3 1C of cooling provided precipitation was reduced by 35% and lapse rate changed. This cooling is less than the 6–8 1C cooling inferred from LGM pollen. r 2005 Elsevier Ltd and INQUA. All rights reserved.
Improving on-line neural networks backpropagation convergence speed with mixed pattern-batch learning

The present paper describes an algorithmic technique to speed up weight convergence in neural networks on-line training. Standard pattern backpropagation is modified to train the neural network over a time window of samples and not one sample only, so that a faster weight convergence may be achieved. The use of such training technique is explained in an adaptive control task and problems related to validation of real functional approximation are investigated.
Elusive isotopic properties of deglacial meltwater spikes into the North Atlantic: example of the final drainage of Lake AgassizThis article is one of a series of papers published in the Special Issue on the theme Polar Climate Stability Network.

The impact of the final drainage of Lake Agassiz, some 8.4 ka ago on the Atlantic Meridional Overturning Circulation is still debated. The lack of isotopic response in planktic foraminifer records at the outlet of the drainage channel constitutes a puzzling element in this debate. To estimate the response of the 18O–salinity relationship in ocean surface waters to drainage, we use a core raised from southeast Hudson Bay to document δ18O values of lake waters, immediately prior to drainage. Valves of Candona sp. (an ostracod) from lacustrine varved-sediments underlying marine clays, yielded δ18O values clustered around –20.5‰ (versus VPDB (Vienna PeeDee Belemnite)). Assuming a lake bottom temperature of about 0 °C, an isotopic composition of –25‰ (versus VSMOW (Vienna standard mean ocean water)) is calculated for paleolake waters, not unlike values reported for earlier stages of Lake Agassiz. This value is only slightly more negative than those estimated for Laurentide Ice Sheet (LIS) meltwaters during the.
Streamflow Data from Small Basins: A Challenging Test to High-Resolution Regional Climate Modeling

AbstractLand surface models and large-scale hydrological models provide the basis for studying impacts of climate and anthropogenic changes on continental- to regional-scale hydrology. Hence, there is a need for comparison and validation of simulated characteristics of spatial and temporal dynamics with independent observations. This study introduces a novel validation framework that relates to common hydrological design measures. The framework is tested by comparing anomalies of runoff from a high-resolution climate-model simulation for Europe with a large number of streamflow observations from small near-natural basins. The regional climate simulation was performed as a “poor man’s reanalysis,” involving a dynamical downscaling of the 40-yr European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-40) with the Danish “HIRHAM5” model. For 19 different anomaly levels, two indices evaluate the temporal agreement (i.e., the occurrence and frequency of dry and wet events based on daily anomalies), .
Analysis of ENVISAT ASAR data for forest parameter retrieval and forest type classification—a case study over deciduous forests of central India

The present paper gives an account of potential of Environment Satellite‐Advanced Synthetic Aperture Radar (ENVISAT‐ASAR) C‐band data in forest parameter retrieval and forest type classification over deciduous forests of Tadoba Andhari Tiger Reserve (TATR), central India. Ground data on phyto‐sociology and Leaf Area Index (LAI) over the study area was collected in 23 sampling points (20m×20m) over the study area. Phyto‐sociological data collected over the study area was used to compute plot‐wise biometric parameters like basal area, volume, stem density and dominant height. ENVISAT ASAR data covering the study area, pertaining to 24 November 2005, has been geo‐referenced and digital number (DN) values were converted to radar backscatter values. Regression analysis between backscatter and the retrieved biometric variables has been done to explain the relationships between SAR backscatter and forest parameters. Analysis showed a significant correlation between backscatter and biometric parameters and backscatter values typically increased with increase in basal area, volume, stem density and dominant height. The scatter observed between ASAR backscatter and stem density, basal area and dominant height suggested limitation of C‐band data in estimating biometric variables in heterogeneous forest systems. Further, ASAR data was used in conjunction with Indian Remote sensing Satellite (IRS‐P6)—Linear Imaging Self Scanner (LISS) III data of 16 October 2004 to classify the study area into different land use/land cover (LU/LC) classes. Various texture and adaptive filters were applied on ASAR image to reduce speckle noise and enhance image features. An attempt is made to merge ASAR image with LISS‐III to enhance feature discrimination. Training sets corresponding to the ground data have been used to derive confusion matrices for the ASAR and LISS‐III images. Results suggested better discrimination of vegetation types in the merged data suggesting the possible use of ASAR data in forest type discrimination.
Lariosaurus xingyiensis (Reptilia: Sauropterygia) from the Triassic of China

The anatomy of a specimen of Lariosaurus xingyiensis (IVPP V 11866) from the Middle Triassic of southern China is described in detail. The specimen ranks among the best preserved of its genus. Specimen IVPP V 11866 is the first unequivocal record of the occurrence of Lariosaurus in the Triassic of southern China, indeed the first record of this genus outside the western Tethyan province. A cladistic analysis using parsimony found IVPP V 11866 to represent the sister taxon of Lariosaurus calcagnii from the Middle Triassic of the southern Alps. This result reinforces the signal for western Tethyan paleobiogeographic relationships of the Triassic marine reptiles from southern China.
Conspiracy Thinking and State-Trait Anxiety in Young Polish Adults

The relationships among conspiracy thinking and state and trait anxiety were examined with 118 high school students who were assessed using the Conspiracy Beliefs Scale and the State-Trait Anxiety Inventory. Among boys there was a positive correlation between scores on A-Trait and the conspiracy thinking (r =.39) whereas among girls there was a negative correlation between these scores (r = −.32).
HerMES: A STATISTICAL MEASUREMENT OF THE REDSHIFT DISTRIBUTION OF HERSCHEL-SPIRE SOURCES USING THE CROSS-CORRELATION TECHNIQUE

The wide-area imaging surveys with the Herschel Space Observatory at submillimeter (sub-mm) wavelengths have now resulted in catalogs of the order of one-hundred-thousand dusty, starburst galaxies. These galaxies capture an important phase of galaxy formation and evolution, but, unfortunately, the redshift distribution of these galaxies, N(z), is still mostly uncertain due to limitations associated with counterpart identification at optical wavelengths and spectroscopic follow-up. We make a statistical estimate of N(z) using a clustering analysis of sub-mm galaxies detected at each of 250, 350 and 500 μm from the Herschel Multi-tiered Extragalactic Survey centered on the Boötes field. We cross-correlate Herschel galaxies against galaxy samples at optical and near-IR wavelengths from the Sloan Digital Sky Survey, the NOAO Deep Wide Field Survey, and the Spitzer Deep Wide Field Survey. We create optical and near-IR galaxy samples based on their photometric or spectroscopic redshift distributions and test the accuracy of those redshift distributions with similar galaxy samples defined with catalogs from the Cosmological Evolution Survey (COSMOS), which has superior spectroscopic coverage. We model the clustering auto- and cross-correlations of Herschel and optical/IR galaxy samples to estimate N(z) and clustering bias factors. The S350 > 20 mJy galaxies have a bias factor varying with redshift as b(z) = 1.0+1.0− 0.5(1 + z)1.2+0.3− 0.7. This bias and the redshift dependence is broadly in agreement with galaxies that occupy dark matter halos of mass in the range of 1012 to 1013 M☉. We find that galaxy selections in all three Spectral and Photometric Imaging Receiver (SPIRE) bands share a similar average redshift, with 〈z〉 = 1.8 ± 0.2 for 250 μm selected samples, and 〈z〉 = 1.9 ± 0.2 for both 350 and 500 μm samples, while their distributions behave differently. For 250 μm selected galaxies we find the a larger number of sources with z ⩽ 1 when compared with the subsequent two SPIRE bands, with 350 and 500 μm selected SPIRE samples having peaks in N(z) at progressively higher redshifts. We compare our clustering-based N(z) results to sub-mm galaxy model predictions in the literature, and with an estimate of N(z) using a stacking analysis of COSMOS 24 μm detections.
Effects of ambient versus reduced UV‐B radiation on high arctic Salix arctica assessed by measurements and calculations of chlorophyll a fluorescence parameters from fluorescence transients

A UV-B exclusion-experiment was conducted in the high Arctic Zackenberg, NE Greenland, in which Salix arctica leaves during most of the growing season were fixed perpendicular to the solar zenith angle, thereby receiving maximal solar radiation. Covered with Teflon and Mylar foil, the leaves received approximately 90 and 40% of the ambient UV-B irradiance, respectively. The effects were examined through recordings of chlorophyll a fluorescence transients, determination of biomass and analysis of total carbon and nitrogen content and amount of soluble flavonoids in the leaves. The processing of light was analysed by means of the chlorophyll a fluorescence transient, using the so-called JIP test, as evolved by Reto J. Strasser and his coworkers. Reduction of the UV-B irradiance caused a rise in many of the fluorescence parameters during July, but not in August (late season). Thus increases in the efficiency that an absorbed photon will be trapped by the PSII reaction centre with the resultant reduction of Q A to Q A - (ETo/ABS = F V /F M ) and the efficiency that an electron residing on Q A - will enter the intersystem electron transport chain (ET o /TR o ) were observed in reduced UV-B. Moreover, estimated per cross-section of leaf sample, the number of active PSII reaction centres (RC/ CS M ) and electron transport rate (ET M /CS M ) and all performance indexes (PI ABS , PI CSo and PI CSm ) were increased in reduced UV-B. The total soluble flavonoid content was highest in ambient UV-B. The treatment effects on fluorescence parameters that were directly measured (e.g. F O and F M ) and those that were derived (e.g. quantum efficiencies, parameters per PSII reaction centres and per cross-section of leaf sample) are discussed in relation to one another, in relation to daily and seasonal variation, and from the perspective of evaluating the relative importance of UV-B of donor and acceptor side capacity in Photosystem II. In conclusion, the experimental set-up and non-invasive measurements proved to be a sensitive method to screen for effects of UV-B stress.
Quality of Life after Brain Injury (QOLIBRI): scale development and metric properties.

The consequences of traumatic brain injury (TBI) for health-related quality of life (HRQoL) are poorly investigated, and a TBI-specific instrument has not previously been available. The cross-cultural development of a new measure to assess HRQoL after TBI is described here. An international TBI Task Force derived a conceptual model from previous work, constructed an initial item bank of 148 items, and then reduced the item set through two successive multicenter validation studies. The first study, with eight language versions of the QOLIBRI, recruited 1528 participants with TBI, and the second with six language versions, recruited 921 participants. The data from 795 participants from the second study who had complete Glasgow Coma Scale (GCS) and Glasgow Outcome Scale (GOS) data were used to finalize the instrument. The final version of the QOLIBRI consists of 37 items in six scales (see Appendix ). Satisfaction is assessed in the areas of "Cognition," "Self," "Daily Life and Autonomy," and "Social Relationships," and feeling bothered by "Emotions," and "Physical Problems. " The QOLIBRI scales meet standard psychometric criteria (internal consistency, alpha = 0.75-0.89, test-retest reliability, r(tt) = 0.78-0.85). Test-retest reliability (r(tt) = 0.68-0.87) as well as internal consistency (alpha = 0.81-0.91) were also good in a subgroup of participants with lower cognitive performance. Although there is one strong HRQoL factor, a six-scale structure explaining additional variance was validated by exploratory and confirmatory factor analyses, and with Rasch modeling. The QOLIBRI is a new cross-culturally developed instrument for assessing HRQoL after TBI that fulfills standard psychometric criteria. It is potentially useful for clinicians and researchers conducting clinical trials, for assessing the impact of rehabilitation or other interventions, and for carrying out epidemiological surveys.