Miracle-dz/UniFAR-FTUs huggingface dataset:
ArrayBridge: Interweaving Declarative Array Processing in SciDB with Imperative HDF5-Based Programs

Scientists are increasingly turning to datacenter-scale computers to analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC programs even for the most mundane queries. This impedance mismatch is due to the cumbersome and costly data format conversions that are needed to use scientific data management tools, such as SciDB, in an HPC setting. Our goal is to make declarative array manipulations from SciDB interoperable with imperative, file-centric analyses from HDF5-based programs. This paper describes ArrayBridge, a bi-directional array view mechanism for the HDF5 file format, that allows scientists to use SciDB, TensorFlow and HDF5-based analysis code in the same file-centric pipeline without converting between file formats. In addition to fast querying over HDF5 array objects, ArrayBridge produces arrays in the HDF5 file format as easily as it can read from it. ArrayBridge also supports time travel queries from imperative codes through the unmodified HDF5 API, and automatically deduplicates between versions for space efficiency. Our performance evaluation in a large scientific computing facility shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine and is 3× faster than TileDB.
Human umbilical cord mesenchymal stem cells facilitate the up‐regulation of miR‐153‐3p, whereby attenuating MGO‐induced peritoneal fibrosis in rats

MiRNAs contribute greatly to epithelial to mesenchymal transition (EMT) of peritoneal mesothelial cells (PMCs), which is a crucial step in peritoneal fibrosis (PF). In this study, we tried to profile whether miRNA expression differences exist after human umbilical cord mesenchymal stem cells (hUCMSCs) treatment in PF rats and investigate the possible role of miR‐153‐3p involved in anti‐EMT process. We randomly assigned 34 rats into three groups: control group (Group Control), MGO‐induced PF rats (Group MGO) and hUCMSCs‐treated rats (Group MGO + hUCMSCs). MiRNA microarrays and real‐time PCR analyses were conducted in three groups. α‐SMA, Snail1 and E‐cadherin expression were detected by Western blot. Luciferase reporter assays were used to detect the effects of miR‐153‐3p overexpression on Snai1 in rat peritoneal mesothelial cells (RPMCs). We identified differentially expressed miRNAs related to EMT, in which miR‐153‐3p demonstrated the greatest increase in Group MGO + hUCMSCs. Transient cotransfection of miR‐153‐3p mimics with luciferase expression plasmids resulted in a significant repression of Snai1 3′‐untranslated region luciferase activity in RPMCs. These studies suggest that miR‐153‐3p is a critical molecule in anti‐EMT effects of hUCMSCs in MGO‐induced PF rats. MiR‐153‐3p might exert its beneficial effect through directly targeting Snai1.
Prototype of Chinese Macroeconomic Management Information System

Chinese Macroeconomic Management Information System is one of the most important e-Government projects, which collects economic information from government departments, establishes the database and data warehouse, and makes economic analysis reports for government departments to make decisions about great economic policies. In this paper we introduce a prototype which can experiment some critical technologies involved in this system, such as information services using a portal website, query and management of large scale database and data warehouse, data analysis and presentation, and the unstructured information management in the remote literature warehouse.
Objective motor assessment for personalized rehabilitation of upper extremity in brain injury patients.

BACKGROUND The increasing number of patients with acquired brain injury and the current subjectivity of the conventional upper extremity (UE) assessment tests require new objective assessment techniques. OBJECTIVE This research proposes a novel objective motor assessment (OMA) methodology based on the Fugl-Meyer assessment (FMA). The goals are to automatically calculate the objective scores (OSs) of FMA-UE movements (as well as a global OS) and to interpret the estimated OSs. METHODS Fifteen patients participated in the study. The OMA algorithm was designed to detect small-scale variations in UE movements. The OSs for 14 FMA-UE movements and the global OSs were automatically calculated using the algorithm and evaluated by 2 therapists. The interpretation of the global OSs was performed at 3 levels: by item, movement and globally. RESULTS The global OSs calculated by our algorithm had a significant correlation with the therapists' scores (0.783 and 0.938, p < 0.01). All OSs for each movement were correlated with the scores given by the therapists. The correlation coefficient can reach values as high as 0.981 (p < 0.01). CONCLUSIONS We provide a new objective assessment tool for therapists to help them improve the diagnostic accuracy and to achieve a more personalized and potentially effective physical rehabilitation of brain injury patients.
Development and Analysis of Synchronization Detection Framework in TDD

Testing method using Test-Driven Development has its specific features and requirements. However, the performance of synchronization has not yet been studied in the environment of test cases which is handled in different quantity concurrently. So, in this article, a framework is developed to test the test case in two ways: multi-thread and single-thread. By means of distributed computing and concurrent testing, a testing model is built and analyzed further. Finally, the experiments shows the utilization rate of the CPU and the run time of system depending on the number of threads as well as the test cases shared by each thread. The better test method is shown as the number of test cases is setup. Furthermore, it can be applied to software and hardware environment in different platforms.
Is Two Enough?: ! Studying Benefits, Barriers, and Biases of Multi-Tablet Use for Collaborative Visualization

A sizable part of HCI research on cross-device interaction is driven by the vision of users conducting complex knowledge work seamlessly across multiple mobile devices. This is based on the Weiserian assumption that people will be inclined to distribute their work across multiple ``pads' if such are available. We observed that this is not the reality today, even when devices were in abundance. We present a study with 24 participants in 12 dyads completing a collaborative visualization task with up to six tablets. They could choose between three different visualization types to answer questions about economic data. Tasks were designed to afford simultaneous use of tablets, either with linked or independent views. We found that users typically utilized only one tablet per user. A quantitative and qualitative analysis revealed a ``legacy bias' that introduced barriers for using more tablets and reduced the overall benefit of multi-device visualization.
Range determination for mobile robots using an omnidirectional camera

We propose a method for computing the absolute distances to static obstacles using a single omnidirectional camera. The method is applied to mobile robots. We achieve this without restricting the application to predetermined translations or the use of artificial markers. In contrast to prior work, our method is able to build absolute scale 3D without the need of a known baseline length, traditionally acquired by odometry. Instead we use the ground plane assumption together with the camera system's height to determine the scale factor. Using only one omnidirectional camera our method is cheaper, more informative and more compact than the traditional methods for distance determination, especially when a robot is already equipped with a camera for e.g. navigation. It also provides more information since it determines distances in a 3D space instead of in one plane. The experiments show promising results. The algorithm is indeed capable of determining the distances in meters to features and obstacles and is able to locate all major obstacles in the scene.
REACTOR DESIGN AND OPERATION VARIABLES TO IMPROVE MIXED ALGAL BIOMASS PRODUCTIVITY AND SOLIDS SEPARATION: AN EXAMINATION OF OPERATION PARAMETERS, DENSITY, AND SETTLEABILITY

Algae have been identified as a source of renewable, clean energy, with much research being devoted to identifying high energy yield algae, energy extraction methods, and reactor design with mono-cultures of algae, but little research has been done on reactor design and operational conditions with mixed cultures of algae to improve productivity and solids separation. The objective of this study was to determine if the settling characteristics of mixed algal cultures can be enriched or improved through manipulation of reactor design characteristics by incorporating cyclic settling or floating phases into operation, timing of light/dark cycles, and/or control of the solids and hydraulic residence time. Photobioreactors constructed of cast acrylic were operated as sequencing batch reactors. Each reactor was run with identical feed, light/dark cycle, and working volume. Biomass measurements were taken regularly to measure growth and productivity. Density measurements were taken to observe operation conditions effects on solids separation. The sludge volume index (SVI) was used to assess the degree of solids separation in each reactor. Selection for algal biomass with good settling or flotation
Association between Modified Body Mass Index and 30-Day and 1-Year Mortality after Intensive Care Unit Admission: A Retrospective Cohort Study

Because conventional body mass index (cBMI) does not reflect fluid accumulation, modified BMI (mBMI, serum albumin multiplied by cBMI) is a more accurate measure of malnutrition status. This study aimed to determine whether mortality after intensive care unit (ICU) admission was associated with cBMI, mBMI, and/or serum albumin levels. The medical records of patients who were admitted to a tertiary hospital ICU between 1 January 2012 and 31 July 2016 were retrospectively reviewed. In total, 6169 ICU-admitted patients were included in the analyses. Multivariate Cox regression analyses revealed that low cBMI, mBMI and albumin level were significantly associated with 30-day and 1-year mortality after ICU admission (hazard ratio < 1.0, p < 0.05). The adjusted area under the curve (AUC) of mBMI for 1-year mortality was significantly higher than that of cBMI (p < 0.001), but not significantly different from that of albumin level (p = 0.098). Low values of mBMI, cBMI and albumin were independently associated with 30-day and 1-year mortality after ICU admission. Combining cBMI and albumin (mBMI) did not increase the validity of the AUC of albumin for 1-year mortality after ICU admission. Our study showed that serum albumin alone, rather than mBMI (combining cBMI), is recommended in predicting mortality among ICU patients.
Non-acute (residual) neurocognitive effects of cannabis use: A meta-analytic study

The possible medicinal use of cannabinoids for chronic diseases emphasizes the need to understand the long-term effects of these compounds on the central nervous system. We provide a quantitative synthesis of empirical research pertaining to the non-acute (residual) effects of cannabis on the neurocognitive performance of adult human subjects. Out of 1,014 studies retrieved using a thorough search strategy, only 11 studies met essential a priori inclusion criteria, providing data for a total of 623 cannabis users and 409 non- or minimal users. Neuropsychological results were grouped into 8 ability domains, and effect sizes were calculated by domain for each study individually, and combined for the full set of studies. Using slightly liberalized criteria, an additional four studies were included in a second analysis, bringing the total number of subjects to 1,188 (i.e., 704 cannabis users and 484 non-users). With the exception of both the learning and forgetting domains, effect size confidence intervals for the remaining 6 domains included zero, suggesting a lack of effect. Few studies on the non-acute neurocognitive effects of cannabis meet current research standards; nevertheless, our results indicate that there might be decrements in the ability to learn and remember new information in chronic users, whereas other cognitive abilities are unaffected. However, from a neurocognitive standpoint, the small magnitude of these effect sizes suggests that if cannabis compounds are found to have therapeutic value, they may have an acceptable margin of safety under the more limited conditions of exposure that would likely obtain in a medical setting. (JINS, 2003, 9, 679–689.)
Toll-Like Receptor Agonists Synergize with CD40L to Induce Either Proliferation or Plasma Cell Differentiation of Mouse B Cells

In a classical dogma, pathogens are sensed (via recognition of Pathogen Associated Molecular Patterns (PAMPs)) by innate immune cells that in turn activate adaptive immune cells. However, recent data showed that TLRs (Toll Like Receptors), the most characterized class of Pattern Recognition Receptors, are also expressed by adaptive immune B cells. B cells play an important role in protective immunity essentially by differentiating into antibody-secreting cells (ASC). This differentiation requires at least two signals: the recognition of an antigen by the B cell specific receptor (BCR) and a T cell co-stimulatory signal provided mainly by CD154/CD40L acting on CD40. In order to better understand interactions of innate and adaptive B cell stimulatory signals, we evaluated the outcome of combinations of TLRs, BCR and/or CD40 stimulation. For this purpose, mouse spleen B cells were activated with synthetic TLR agonists, recombinant mouse CD40L and agonist anti-BCR antibodies. As expected, TLR agonists induced mouse B cell proliferation and activation or differentiation into ASC. Interestingly, addition of CD40 signal to TLR agonists stimulated either B cell proliferation and activation (TLR3, TLR4, and TLR9) or differentiation into ASC (TLR1/2, TLR2/6, TLR4 and TLR7). Addition of a BCR signal to CD40L and either TLR3 or TLR9 agonists did not induce differentiation into ASC, which could be interpreted as an entrance into the memory pathway. In conclusion, our results suggest that PAMPs synergize with signals from adaptive immunity to regulate B lymphocyte fate during humoral immune response.
Survey: Big Data Application in Biomedical Research

In recent years, the emergence of diverse applications created a plethora of data and immense sources that can be applied in varying areas of the industry worldwide escalating its capabilities including biomedicine. Subsequently, analytical tools loomed to leverage the availability of massive data to analyze and elicit meaningful information to improve biomedical research and enhance healthcare systems. Algorithms applied in these analytical tools supplements the prognosis of diseases and personalized treatment of fatal diseases. This survey will evaluate algorithms used in bio medical research for personalized precision medicine, dissect the characteristics that made breakthrough in improving the efficiency of the analytical tool and identify the possible applicability in other diseases. It will focus on the machine learning and deep learning algorithms, both supervised and unsupervised that is applied in terminal diseases.
Semiconductor nanowire based coherent light sources: temporal dynamics and tunability

Semiconductor nanowires (NWs) offer exceptional optical properties such as efficient waveguiding of light despite their subwavelength diameter. These properties are strongly related to the semiconductor material and their morphology. Additionally, semiconductor NWs inherently offer all basic components of a laser system including robust, high optical gain and a beneficial Fabry-Perot resonator structure. Thus, they are considered as one of the smallest coherent light sources available for different visionary concepts in recent research on nanophotonics, nanosensing and nanspectroscopy. Laser oscillations in single NWs have only been achieved in a pulsed operation mode so far, as the off times between the optical pump pulses allows the thermal budget introduced by the optical pumping to dissipate in order to avoid a successive material degradation. In order to establish the continuous wave (cw) emission mode in single NWs, a semiconductor material of exceptional high optical gain and an excellent NW resonator morphology is required. Both challenges can be accomplished by using CdS NWs synthesized by the vapor-liquid-solid (VLS) mechanism using Sn as catalyst. Knowing the fundamental laser dynamics of semiconductor NWs will enable the exploitation of their full potential as nanoscaled coherent light sources. The respective time scales for laser onset time and pulse width are in the range of few hundred femtoseconds up to few picoseconds and can be measured by a novel double-pump technique. In addition, both characteristic times can be adjusted by a proper choice of semiconductor material, pump energy and optical configuration. The field distribution within a NW laser can be adjusted between single and multi-transverse mode operation by varying the NW diameter. Thin NWs below the critical diameter for multimode waveguiding emit laser emission of the fundamental mode, whereas NWs with larger diameters clearly show multimode operation. Furthermore, the transverse mode structure strongly affects the light-matter interaction and the NW laser dynamics.
Forehead Morphology Pattern: Does it indicate the Potential Existence of the so-called Forehead Print?

Forehead is a part of the human body that never been used in forensics or studied for its potential usefulness in forensics. No one ever talked about the variability of forehead morphology among individuals or how can forehead and/or its impres- sion potentially be used for forensic individual identification. In the present study, forehead images were taken for the foreheads of 800 unrelated consented male subjects, volunteers of the Egyptian origin, ranging in age from 10 to over 70 years. Careful examination of the collected forehead images was conducted by the naked eye observation for the existence of forehead wrinkles or any thing else on the forehead that can be specific for the forehead of the individual such as dermatological lesion/s, recent wound or scar of old wound or anything else that can be of value in the individual identification. Forehead wrinkles were examined for the number, shape, position and direction. Forehead could be categorized according to the morphology of the wrinkling pattern that they have. There are two types of forehead wrinkles, horizontal and vertical. Forehead examined for the age of appearance of forehead wrinkles and for the persistence of the wrinkling pattern. Forehead wrinkles have proven that they are persistent and when they appear, they remain throughout the lifetime. Forehead wrinkles have been examined for their shape during different expressions to see what they look like during these expressions. Foreheads were also examined to see what one can rely upon in identification of forehead, especially when the forehead wrinkles are absent.
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

Abstract Background As one of the most popular and valuable commercial marine fishes in China and East Asian countries, the Chinese black porgy (Acanthopagrus schlegelii), also known as the blackhead seabream, has some attractive characteristics such as fast growth rate, good meat quality, resistance to diseases, and excellent adaptability to various environments. Furthermore, the black porgy is a good model for investigating sex changes in fish due to its protandrous hermaphroditism. Here, we obtained a high-quality genome assembly of this interesting teleost species and performed a genomic survey on potential genes associated with the sex-change phenomenon. Findings We generated 175.4 gigabases (Gb) of clean sequence reads using a whole-genome shotgun sequencing strategy. The final genome assembly is approximately 688.1 megabases (Mb), accounting for 93% of the estimated genome size (739.6 Mb). The achieved scaffold N50 is 7.6 Mb, reaching a relatively high level among sequenced fish species. We identified 19 465 protein-coding genes, which had an average transcript length of 17.3 kb. By performing a comparative genomic analysis, we found 3 types of genes potentially associated with sex change, which are useful for studying the genetic basis of the protandrous hermaphroditism. Conclusions We provide a draft genome assembly of the Chinese black porgy and discuss the potential genetic mechanisms of sex change. These data are also an important resource for studying the biology and for facilitating breeding of this economically important fish.
Relative index finger length as a sex-influenced trait in man.

ALTHOUGH a genetic basis has been determined for numerous abnormalities of the hand and foot, relatively little attention has been given to the inheritance of normal variations in shape and structure. One of the most frequently reported normal variations in the human hand is the length of the index finger as compared with the ring finger. Ecker (1875) noted that three manifestations of relative finger length may be discerned in the living model: index finger shorter than ring finger (2 < 4); index finger equal in length to ring finger (2 = 4); and index finger longer than ring finger (2 > 4). Many of the earlier workers failed to recognize this variability in relative index finger length. Gerdy (1829) stated that the index finger is always shorter than the ring finger, while according to Carus (1853) and Humphry (1861), the index finger exceeds the ring finger in length. Langer (1865) declared that the index finger is shorter than or nearly equal to the ring finger. Alix (1867), Grining (1886), Baker (1888), Schultz (1926), and Wood-Jones (1920, 1941) point out that although the index finger is usually shorter than the ring finger, it may in certain instances exceed the length of the ring finger. Ecker (1875), Mantegazza (1877), GrUning (1886), Baker (1888), Volotzkoy (1924), and Huizinga (1949) each found that all three formulas occur in both sexes but that a relatively long index finger is found more frequently in females than in males. George (1930) studied a Canadian population and found that 2 < 4 is the most frequent formula in males while a 2 > 4 formula predominates in females. Volotzkoy (1924), Schultz (1926) and Huizinga (1949) have noted that the various formulas may also be observed in fetuses. Although Kloepfer (1946) has suggested that the variations in relative index finger length may be hereditary, no attempt has been made to establish