Miracle-dz/UniFAR-FTUs huggingface dataset:
Setting Inventory Levels in a Bike Sharing Network

Bike sharing systems (BSSs) allow customers to rent bicycles at automatic rental stations distributed throughout a city, use them for a short period of time, and return them to any station. One of the major issues that BSS operators must address is nonhomogeneous asymmetric demand processes. These demand processes create an inherent imbalance, thus leading to shortages either of bicycles when users are attempting to rent them and of vacant lockers when users are attempting to return them. The predominant approach taken by operators to cope with this difficulty is to reposition bicycles to rebalance the inventory levels at the different stations. Most repositioning studies assume that a target inventory level or range of inventory levels is known for each station. In this paper, we focus on determining the correct target level for repositioning according to a well-defined objective. This is a challenging task because of the nature of the user behavior that creates the interactions among the inventory level.
The fundus photo has met its match: optical coherence tomography and adaptive optics ophthalmoscopy are here to stay

Over the past 25 years, optical coherence tomography (OCT) and adaptive optics (AO) ophthalmoscopy have revolutionised our ability to non‐invasively observe the living retina. The purpose of this review is to highlight the techniques and human clinical applications of recent advances in OCT and adaptive optics scanning laser/light ophthalmoscopy (AOSLO) ophthalmic imaging.
Assessment of lipid profile changes with respect to severity of liver dysfunction in cirrhosis of liver

Objectives: Cirrhosis of Liver is the end stage result of many etiologies affecting Liver. It is important to assess severity since management varies accordingly. Liver plays a central role in lipid metabolism, lipids are known to be altered. Our aim was to assess severity of Cirrhosis by Child Pugh scoring and correlating with Lipid levels. We attempted to know the pattern of lipid abnormalities and assessed its role in prognostication. Methods: This was a Cross sectional study done at Bapuji hospital, a teritary care center at Davangere. 100 cirrhosis patients fulfilling inclusion criteria, were included in the study. Results: Levels of cholesterol, LDL, HDL and VLDL in cases were significantly reduced when compared to control group (P<0.000). Levels of TGL were marginally reduced in cases (P<0.05). Total Cholesterol (P <.001), TGL (P<.02), HDL (P < .05) and LDL (P<.000) showed a significant negative correlation with Severity of Cirrhosis. VLDL had no correlation with the severity of Cirrhosis. Conclusion: From this study, it was found that cholesterol, LDL, HDL and VLDL were significantly lower. The hypolipidemia may be due to decreased synthesis of Apolipoproteins in studies. Reduced HDLc could be attributed to decrease production of LCAT, apoliportien I and II. Hypolipidemia (except VLDL) was correlating to the severity of Cirrhosis. This is comparable to the earlier studies. In conclusion, dyslipidemia exists in patients with cirrhosis. Thus serum Lipid profile may serve as a sensitive indicator of Liver Dysfunction in Cirrhosis.
CGH analysis of radon‐induced rat lung tumors indicates similarities with human lung cancers

Epidemiological studies have shown that inhalation of radon, a radioactive gas, is associated with an increased risk for lung cancer. We have developed a model of radon‐induced rat lung tumors to characterize cytogenetic and molecular events involved in radon‐induced lung tumorigenesis. Using comparative genomic hybridization (CGH), gains and losses of genetic material were investigated in a series of 13 carcinomas and four adenomas of the lung. Frequent losses occurred at 4q12–21, 5q11–33, and 15q, which are homologous to human chromosome (HSA) bands 7q21–36, 1p31–36/9p21–31, and 13q14.1–14.3/3p14.2, respectively. These regions are frequently (30–80%) deleted in human lung cancer and contain tumor suppressor genes or proto‐oncogenes such as MET, CDKN2A/p16/MTS1, CDKN2B/p15/MTS2, FHIT, and RB1 or yet to be identified genes. Frequent gains involved 6, 7q34–qter, and 19q; chromosomes 6 and 7 being homologous to human 2p21–25 and 8q21–24 where the MYCN and MYC oncogenes are located. The genetic similarities between rat and human lung cancer suggest common underlying mechanisms for tumor evolution in both species. Moreover, cytogenetic and molecular genetic analyses of radon‐induced rat lung tumors could help to better understand the development and progression of radon‐induced lung cancer in man. Genes, Chromosomes and Cancer 29:1–8, 2000. © 2000 Wiley‐Liss, Inc.
Crystal structure of the MYB domain of the RAD transcription factor from Antirrhinum majus

Introduction. The RAD gene of Antirrhinum majus encodes a single-repeat MYB transcription factor that is implicated in the control of floral asymmetry. Herein we present the crystal structure of the MYB domain of the RAD protein determined using the anomalous signal of iodide and refined to a resolution of 1.9 Å. This constitutes the first X-ray structure of a single-repeat MYB protein. The structure conforms to the three-helix bundle fold of the canonical MYB domain, although the third helix is notably longer. Several developmental genes have been identified in Antirrhinum majus (garden snapdragon) that are implicated in the control of asymmetric floral architecture. Sequence analysis suggests that two of these genes, RADIALIS (RAD) and DIVARICATA (DIV), encode putative MYB transcription factors, this being consistent with their proposed signaling roles. MYB transcription factors are ubiquitous in eukaryotes, most notably in plants, and contain one or more copies of the so-called MYB DNAbinding domain. MYB domains are approximately 50 residues in length, highly variable in sequence, but are often characterized by three regularly spaced Trp residues. MYB proteins can be split into three subfamilies depending on whether they have one, two or three imperfect repeats of the MYB domain. Most MYB proteins from vertebrates consist of three imperfect repeats (R1, R2, and R3), but plants contain large numbers of two repeat (R2 and R3) MYBs. In some cases, however, only one MYB-like domain is present. The DIV protein contains two MYB-like domains, whilst the RAD protein contains only one. The latter is closely related in sequence to the N-terminal MYB domain of DIV, suggesting that RAD may have evolved through a C-terminal deletion of a DIV-like ancestral protein. RAD promotes dorsal identity of the flower, whereas DIV promotes ventral identity. It is thought that RAD is activated in the dorsal region of the developing flower, which then inhibits the activity of DIV, by either competitively binding to DIV’s target DNA sequences or to proteins that interact with DIV. So far, DNA binding functions for both RAD and DIV have yet to be demonstrated experimentally, and the possibility exists that they only bind to DNA as complexes with other proteins. To date, there are relatively few structures of MYB proteins in the Protein Data Bank (PDB), despite their prevalence in nature, possibly reflecting inherent problems in over expressing and crystallizing this family of proteins. Moreover, the majority of known structures have been determined using NMR rather than X-ray crystallography. In this article, we report the crystal structure determination of an 8 kDa fragment of the 10.8 kDa RAD protein from Antirrhinum majus that encompasses the entire MYB domain and was determined using the anomalous signal of iodide from X-ray data collected in-house.
Two-link swimming using buoyant orientation

The scallop theorem posits that a two-link system immersed in a fluid at low Reynolds number cannot achieve any net translation via cyclic changes in its hinge angle. Here, we propose an approach to “breaking” this theorem, based on a static separation between the centers of mass and buoyancy in a net neutrally buoyant system. This separation gives the system a natural equilibrium orientation, allowing it to passively reorient without changing shape.
Optical molecular imaging‐guided radiation therapy part 2: Integrated x‐ray and fluorescence molecular tomography

Purpose Differentiating tumor from its surrounding soft tissues is challenging for x‐ray computed tomography (CT). Fluorescence molecular tomography (FMT) can directly localize the internal tumors targeted with specific fluorescent probes. A FMT system was developed and integrated onto a CT‐guided irradiator to improve tumor localization for image‐guided radiation. Methods The FMT system was aligned orthogonal to the cone‐beam CT onboard our previously developed image‐guided small animal arc radiation treatment system (iSMAART). Through rigorous physical registration, the onboard CT provides accurate surface contour which is used to generate three‐dimensional mesh for FMT reconstruction. During FMT experiments, a point laser source perpendicular to the rotating axis was used to excite the internal fluorophores. The normalized optical images from multiple projection angles were adopted for tomographic reconstruction. To investigate the accuracy of the FMT in locating the tumor and recovering its volume, in vivo experiments were conducted on two breast cancer models: MDA‐MB‐231 cancer xenograft on nude mice and 4T1 cancer xenograft on white mice. Both cancer cell lines overexpress the epidermal growth factor receptor (EGFR). A novel fluorescent poly(lactic‐co‐glycolic) acid (PLGA) nanoparticle conjugated with anti‐EGFR was intravenously injected to specifically target the breast cancer cells. Another ex vivo experiment on a mouse bearing a surgically implanted Indocyanine Green‐containing glass tube was conducted, to additionally validate the precision of FMT‐guided radiation therapy. Results The FMT can accurately localize the single‐nodule breast tumors actively targeted with fluorescent nanoparticles with localization error < 0.5 mm calculated between the centers of mass of tumors in FMT and CT. The reconstructed tumor volume in FMT was significantly correlated with that in the iodinated contrast‐enhanced CT (R2 = 0.94, P < 0.001). The FMT was able to guide focal radiation delivery with submillimeter accuracy. Conclusion Using the tumor‐targeting fluorescent probes, the iSMAART with onboard FMT system can accurately differentiate tumors from their surrounding soft tissue, guide precise focal radiation delivery, and potentially assess tumor response in cancer research.
Age‐dependent enhancement of inhibitory synaptic transmission in CA1 pyramidal neurons via GluR5 kainate receptors

Changes in hippocampal synaptic networks during aging may contribute to age‐dependent compromise of cognitive functions such as learning and memory. Previous studies have demonstrated that GABAergic synaptic transmission exhibits age‐dependent changes. To better understand such age‐dependent changes of GABAergic synaptic inhibition, we performed whole‐cell recordings from pyramidal cells in the CA1 area of acute hippocampal slices on aged (24–26 months old) and young (2–4 months old) Brown‐Norway rats. We found that the frequency and amplitude of spontaneous inhibitory postsynaptic current (IPSCs) were significantly increased in aged rats, but the frequency and amplitude of mIPSCs were decreased. Furthermore, the regulation of GABAergic synaptic transmission by GluR5 containing kainate receptors was enhanced in aged rats, which was revealed by using LY382884 (a GluR5 kainate receptor antagonist) and ATPA (a GluR5 kainate receptor agonist). Moreover, we demonstrated that vesicular glutamate transporters are involved in the kainate receptor dependent regulation of sIPSCs. Taken together, these results suggest that GABAergic synaptic transmission is potentiated in aged rats, and GluR5 containing kainate receptors regulate the inhibitory synaptic transmission through endogenous glutamate. These alterations of GABAergic input with aging could contribute to age‐dependent cognitive decline. © 2009 Wiley‐Liss, Inc.
IDS false alarm reduction using an instance selection KNN-memetic algorithm

A K-nearest neighbours-based intrusion detection system uses a training set for classification purpose. The size of this dataset is critical. In fact, if the dataset size is too small, the classification accuracy decreases. However if it is too large, the classification running time might be excessive. This paper describes an instance selection memetic algorithm used for the improvement of IDS classification. The proposed memetic controlled local search MCLS algorithm includes a new local search that allows the orientation and the improvement of the solutions. Besides, the proposed MCLS algorithm enhances the capabilities of the standard KNN classifier in intrusion detection field. The results obtained through experiments on KDD '99 dataset are very satisfactory as they enable the elimination of the false positive alerts while keeping a high detection rate.
A hitchhiker's guide to behavioral analysis in laboratory rodents

Genes and environment are both essential and interdependent determinants of behavioral responses. Behavioral genetics focuses on the role of genes on behavior. In this article, we aim to provide a succinct, but comprehensive, overview of the different means through which behavioral analysis may be performed in rodents. We give general recommendations for planning and performing behavioral experiments in rats and mice, followed by brief descriptions of experimental paradigms most commonly used for the analysis of reflexes, sensory function, motor function and exploratory, social, emotional and cognitive behavior. We end with a discussion of some of the shortcomings of current concepts of genetic determinism and argue that the genetic basis of behavior should be analyzed in the context of environmental factors.
Patients admitted to the ICU for acute exacerbation of COPD: two-year mortality and functional status.

OBJECTIVE To assess ICU patients with COPD, in terms of in-hospital characteristics, two-year mortality and two-year functional status of survivors. METHODS A prospective cohort study involving patients with acute exacerbation of COPD admitted to the ICUs of two hospitals in the city of Porto Alegre, Brazil, between July of 2005 and July of 2006. At two years after discharge, survivors were interviewed by telephone in order to determine Karnofsky scores and scores on a scale regarding activities of daily living (ADL). RESULTS The sample comprised 231 patients. In-hospital mortality was 37.7%, and two-year post-discharge mortality was 30.3%. Of the 74 survivors, 66 were interviewed (89%). The mean age at ICU admission was 74 ± 10 years, and the mean Acute Physiology and Chronic Health Evaluation II score was 18 ± 7. Two or more comorbidities were present in 87.8% of the patients. Of the 66 interviewees, 57 (86.3%) lived at home, 58 (87.8%) were self-sufficient, 12 (18.1%) required oxygen therapy, and 4 (6.1%) still required ventilatory support. There was a significant reduction in the quality of life and autonomy of the survivors, as evidenced by the Karnofsky scores (85 ± 9 vs. 79 ± 11, p = 0.03) and ADL scale scores (29 ± 5 vs. 25 ± 7; p = 0.01), respectively. CONCLUSIONS In this patient sample, two-year mortality was quite high. Although there was a noticeable reduction in the functional status of the survivors, they remained self-sufficient.
Effects of carbohydrate ingestion on gastric emptying and exercise performance.

In an effort to determine the effects of 5 (CHO-5), 6 (CHO-6), and 7.5 (CHO-7.5) percent carbohydrate solutions on gastric emptying and performance, 8 trained male cyclists performed 4 trials of intermittent (7- x ;12-min bout) cycling at 70% VO2max. A final 12-min self-paced "performance" ride was performed on an isokinetic ergometer (Fitron) interfaced with a computer to provide total work output. A water placebo (WP) was used as a control. Each 12-min ride was followed by 3-min rest, during which a drink was consumed (8.5 ml.kg-1; mean total = 1,336 ml.2 h-1). Blood samples were taken at 0, 25, 55, 85, and 115 min for blood glucose analysis. Following the performance ride, gastric residue was obtained by intubation and aspiration. Of the original 1,336 ml ingested during each trial, the volumes emptied by the stomach for the four trials were 1,306 +/- 76, 1,262 +/- 82, 1,288 +/- 75, and 1,278 +/- 77 ml (+/- SE) for WP, CHO-5, CHO-6, and CHO-7.5, respectively. Only the volume in the CHO-5 trial was significantly different from WP. The performance data showed that in all of the CHO trials, significantly more work was produced compared to the WP trial (CHO-5 = 1.98 +/- 0.09 x 10(5) Nm vs WP = 1.83 +/- 0.11 x 10(5) Nm). There were no significant differences in performance between any of the CHO trials. (ABSTRACT TRUNCATED AT 250 WORDS)
Recognition of Kidney Glomerulus by Dynamic Programming Matching Method

Dynamic programming was applied to locate the glomeruli in microscopic images of kidney tissue section. The glomeruli were modeled by a polygon whose sides could be varied within a given range of lengths. The objects were located by determining the best match of the model according to a so-called optimum criterion in which all possible shapes were evaluated at all possible positions in the input image. The best model was selected according to the maximum average gray level. To increase the probability of obtaining a closed contour, a distance criterion was added and the maximum gray-level requirement was relaxed somewhat. The optimum criterion was modified to include a directionality constraint in which the difference in angle between model segments and the edge values in the image was minimized, thereby increasing the performance of the method. A hierarchical multiresolution strategy was used to reduce calculation time. The cyclical property of a contour is also taken into account. >
Insect Virus Proteins (FALPE and p10) Self-Associate To Form Filaments in Infected Cells

ABSTRACT Entomopoxviruses and baculoviruses are pathogens of insects which replicate in the cytoplasm and nuclei of their host cells, respectively. During the late stages of infection, both groups of viruses produce occlusion bodies which serve to protect virions from the external environment. Immunofluorescence and electron microscopy studies have shown that large bundles of filaments are associated with these occlusion bodies. Entomopoxviruses produce cytoplasmic fibrils which appear to be composed of the filament-associated late protein of entomopoxviruses (FALPE). Baculoviruses, on the other hand, yield filaments in the nuclei and cytoplasm of the infected cell which are composed of a protein called p10. Despite significant differences in their sequences, FALPE and p10 have similar hydrophilicity profiles, and each has a proline-rich stretch of amino acids at its carboxyl terminus. Evidence that FALPE and p10 could produce filaments in the absence of other viral proteins is presented. When FALPE was expressed in insect cells from a recombinant baculovirus, filaments similar to those produced by the wild-type Amsacta mooreientomopoxvirus were observed. In addition, when expression plasmids containing FALPE or p10 genes were transfected into Vero monkey kidney cells, filament structures similar to those found in infected insect cells were produced. The manner in which FALPE and p10 subunits interact to form polymers was investigated through deletion and site-specific mutagenesis in conjunction with immunofluorescence microscopy, yeast two-hybrid protein interaction analysis, and chemical cross-linking of adjacent molecules. These studies indicated that the amino termini of FALPE and p10 were essential for subunit interaction. Although deletion of the carboxy termini did not affect this interaction, it did inhibit filament formation. In addition, modification of several potential sites for phosphorylation also abolished filament assembly. We concluded that although the sequences of FALPE and p10 were different, the structural and functional properties of the two polypeptides appeared to be similar.
ESTIMATING PM2.5 IN THE BEIJING-TIANJIN-HEBEI REGION USING MODIS AOD PRODUCTS FROM 2014 TO 2015

Abstract. Fine particulate matter with a diameter less than 2.5 μm (PM2.5) has harmful impacts on regional climate, economic development and public health. The high PM2.5 concentrations in China’s urban areas are mainly caused by the combustion of coal and gasoline, industrial pollution and unknown/uncertain sources. The Beijing-Tianjin-Hebei (BTH) region with a land area of 218,000 km2, which contains 13 cities, is the biggest urbanized region in northern China. The huge population (110 million, 8% of the China’s population), local heavy industries and vehicle emissions have resulted in severe air pollution. Traditional models have used 10 km Moderate-resolution Imaging Spectroradiometer (MODIS) Aerosol Optical Depth (AOD) products and proved the statistical relationship between AOD and PM2.5. In 2014, the 3 km MODIS AOD product was released which made PM2.5 estimations with a higher resolution became possible. This study presents an estimation on PM2.5 distributions in the BTH region from September 2014 to August 2015 by combining the MODIS satellite data, ground measurements of PM2.5, meteorological parameters and social-economic factors based on the geographically weighted regression model. The results demonstrated that the 10 km AOD product provided results with a slightly higher accuracy although the 3 km AOD product could provide more information about the spatial variations of PM2.5 estimations. Additionally, compared with the global regression, the geographically weighed model was able to improve the estimation results.
Viability of the matter bounce scenario in Loop Quantum Cosmology from BICEP2 last data

The CMB map provided by the Planck project constrains the value of the ratio of tensor-to-scalar perturbations, namely r, to be smaller than 0.11 (95 % CL). This bound rules out the simplest models of inflation. However, recent data from BICEP2 is in strong tension with this constrain, as it finds a value r=0.20+0.07-0.05 with 0r= disfavored at 7.0 σ, which allows these simplest inflationary models to survive. The remarkable fact is that, even though the BICEP2 experiment was conceived to search for evidence of inflation, its experimental data matches correctly theoretical results coming from the matter bounce scenario (the alternative model to the inflationary paradigm). More precisely, most bouncing cosmologies do not pass Planck's constrains due to the smallness of the value of the tensor/scalar ratio r⩽ 0.11, but with new BICEP2 data some of them fit well with experimental data. This is the case with the matter bounce scenario in the teleparallel version of Loop Quantum Cosmology.