Miracle-dz/UniFAR-FTUs huggingface dataset:
High Throughput Short Read Alignment via Bi-directional BWT

The advancement of sequencing technologies has made it feasible for researchers to consider many high-throughput biological applications. A core step of these applications is to align an enormous amount of short reads to a reference genome. For example, to resequence a human genome, billions of reads of 35 bp are produced in 1-2 weeks, putting a lot of pressure of faster software for alignment. Based on existing indexing and pattern matching technologies, several short read alignment software have been developed recently. Yet this is still strong need to further improve the speed. In this paper, we show a new indexing data structure called bi-directional BWT, which allows us to build the fastest software for aligning short reads. When compared with existing software (Bowtie is the best), our software is at least 3 times faster for finding unique best alignments, and 25 times faster for finding all possible alignments. We believe that bi-directional BWTis an interesting data structure on its own and couldbe applied to other pattern matching problems.
ClimBSN: Climber performance monitoring with BSN

The recent growth in popularity in sport climbing is partly due to the safe environment provided by indoor climbing walls, particularly for novice climbers. Sport climbing involves a wide range of skills and abilities. The purpose of this paper is to present a wearable sensing platform and an analysis framework for assessing general climbing performance during training. To provide the required freedom of movement, a single miniaturized ear-worn 3D accelerometer-based sensor is used. Independent features derived from the accelerometer data are then translated into climbing-specific measures, such as motion fluidity, strength, as well as endurance. Based on these indices, the overall level of the climber and the associated climbing styles can be quantified.
On integrating orthogonal information retrieval methods to improve traceability recovery

Different Information Retrieval (IR) methods have been proposed to recover traceability links among software artifacts. Until now there is no single method that sensibly outperforms the others, however, it has been empirically shown that some methods recover different, yet complementary traceability links. In this paper, we exploit this empirical finding and propose an integrated approach to combine orthogonal IR techniques, which have been statistically shown to produce dissimilar results. Our approach combines the following IR-based methods: Vector Space Model (VSM), probabilistic Jensen and Shannon (JS) model, and Relational Topic Modeling (RTM), which has not been used in the context of traceability link recovery before. The empirical case study conducted on six software systems indicates that the integrated method outperforms stand-alone IR methods as well as any other combination of non-orthogonal methods with a statistically significant margin.
Cryoprotective effects of low-density lipoproteins, trehalose and soybean lecithin on murine spermatogonial stem cells

Summary Spermatogonial stem cells (SSCs) have the ability to self-renew and offer a pathway for genetic engineering of the male germ line. Cryopreservation of SSCs has potential value for the treatment of male infertility, spermatogonial transplantation, and so on. In order to investigate the cryopreservation effects of different cryoprotectants on murine SSCs, 0.2 M of low-density lipoproteins (LDL), trehalose and soybean lecithin were added to the cryoprotective medium, respectively, and the murine SSCs were frozen at −80°C or −196°C. The results indicated that the optimal recovery rates of murine SSCs in the cryoprotective medium supplemented with LDL, trehalose and soybean lecithin were 92.53, 76.35 and 75.48% at −80°C, respectively. Compared with freezing at −196°C, the optimum temperature for improvement of recovery rates of frozen murine SSCs, cryopreservation in three different cryoprotectants at −80°C, were 17.11, 6.68 and 10.44% respectively. The recovery rates of murine SSCs in the cryoprotective medium supplemented with 0.2 M LDL were significantly higher than that of other cryoprotectants (P < 0.05). Moreover, the recovery rates were demonstrated to be greater at −80°C compared with at −196°C (P < 0.05). In conclusion, 0.2 M of LDL could significantly protect murine SSCs at −80°C. In the freezing–thawing process, LDL is responsible for the cryopreservation of murine SSCs because it can form a protective film at the surface of membranes. However, more research is needed to evaluate and understand the precise role of LDL during the freezing–thawing of SSCs.
Experimental and simulative investigations on stray capacitances and stray inductances of power modules

This paper presents different experimental methods for measuring parasitic capacitances and inductances of direct copper bond (DBC) based power semiconductor modules. The found parasitics are compared with finite element simulations to evaluate their accuracy. A very good match of the simulated and measured stray capacitances is found. The parasitics, which are found via simulations and experiments, are integrated into a full equivalent circuit of the power module that can be used in SPICE simulations. The model is evaluated by a comparison with double pulse measurements for three examplary operating points. Satisfying simulation results of the developed model can be shown for the given operating points.
Prevalence of Incidental Pancreatic Cysts on 3 Tesla Magnetic Resonance

Objectives To ascertain the prevalence of pancreatic cysts detected incidentally on 3-Tesla magnetic resonance imaging (MRI) of the abdomen and correlate this prevalence with patient age and gender; assess the number, location, and size of these lesions, as well as features suspicious for malignancy; and determine the prevalence of incidentally detected dilatation of the main pancreatic duct (MPD). Methods Retrospective analysis of 2,678 reports of patients who underwent abdominal MRI between January 2012 and June 2013. Patients with a known history of pancreatic conditions or surgery were excluded, and the remaining 2,583 reports were examined for the presence of pancreatic cysts, which was then correlated with patient age and gender. We also assessed whether cysts were solitary or multiple, as well as their location within the pancreatic parenchyma, size, and features suspicious for malignancy. Finally, we calculated the prevalence of incidental MPD dilatation, defined as MPD diameter ≥ 2.5 mm. Results Pancreatic cysts were detected incidentally in 9.3% of patients (239/2,583). The prevalence of pancreatic cysts increased significantly with age (p<0.0001). There were no significant differences in prevalence between men and women (p=0.588). Most cysts were multiple (57.3%), distributed diffusely throughout the pancreas (41.8%), and 5 mm or larger (81.6%). In 12.1% of cases, cysts exhibited features suspicious for malignancy. Overall, 2.7% of subjects exhibited incidental MPD dilatation. Conclusions In this sample, the prevalence of pancreatic cysts detected incidentally on 3T MRI of the abdomen was 9.3%. Prevalence increased with age and was not associated with gender. The majority of cysts were multiple, diffusely distributed through the pancreatic parenchyma, and ≥ 5 mm in size; 12.1% were suspicious for malignancy. An estimated 2.7% of subjects had a dilated MPD.
A Multi-Objective Particle Swarm Optimization approach to robotic grasping

Automatic grasp planning is an active field in robotic research. Its main purpose is to find the contact points between the robotic hand and an object in order to grasp it efficiently. As the robotic hand has many degrees of freedom which induce a huge number of solutions, the search for the “best” solution became an optimization problem. The search of such a solution is conducted by a grasp quality measurement which will be called the objective (or fitness) function. This paper proposes a Multi-Objective Particle Swarm Optimization (MOPSO) approach to tackle the grasp planning problem. Its fitness functions are based in two different grasp quality measurements. The MOPSO approach is then tested in HandGrasp simulator with simple objects. The results will be compared with two simple Particle Swarm Optimization (PSO) approaches and demonstrate its performance.
Novel anti‐staphylococcal and anti‐biofilm properties of two anti‐malarial compounds: MMV665953 {1‐(3‐chloro‐4‐fluorophenyl)‐3‐(3,4‐dichlorophenyl)urea} and MMV665807 {5‐chloro‐2‐hydroxy‐N‐[3‐(trifluoromethyl)phenyl]benzamide}

Purpose. The treatment of device‐related infections is challenging and current anti‐microbial compounds have poor anti‐biofilm activity. We aimed to identify and characterize novel compounds effective in the eradication of Staphylococcus aureus biofilms. Methodology. Two novel compounds, MMV665953 {1‐(3‐chloro‐4‐fluorophenyl)‐3‐(3,4‐dichlorophenyl)urea} and MMV665807{5‐chloro‐2‐hydroxy‐N‐[3‐(trifluoromethyl)phenyl]benzamide}, effective in killing S. aureus biofilms, were identified by screening of the open access ’malaria box’ chemical library. The minimum bactericidal concentrations, half‐maximal inhibition concentration (IC50) values and minimal biofilm killing concentrations effective in the killing of biofilm were determined against meticillin‐resistant S. aureus and meticillin‐sensitive S. aureus. Fibrin‐embedded biofilms were grown under in vivo‐relevant conditions, and viability was measured using a resazurin‐conversion assay and confocal microscopy. The potential for the development of resistance and cytotoxicity was also assessed. Results. MMV665953 and MMV665807 were bactericidal against S. aureus isolates. The IC50 against S. aureus biofilms was at 0.15‐0.58 mg l−1 after 24 h treatment, whereas the concentration required to eradicate all tested biofilms was 4 mg l−1, making the compounds more bactericidal than conventional antibiotics. The cytotoxicity against human keratinocytes and primary endothelial cells was determined as IC50 7.47 and 0.18 mg l−1 for MMV665953, and as 1.895 and 0.076 mg l−1 for MMV665807. Neither compound was haemolytic nor caused platelet activation. MMV665953 and MMV665807 derivatives with reduced cytotoxicity exhibited a concomitant loss in anti‐staphylococcal activity. Conclusion. MMV665953 and MMV665807 are more bactericidal against S. aureus biofilms than currently used anti‐staphylococcal antibiotics and represent a valuable structural basis for further investigation in the treatment of staphylococcal biofilm‐related infections.
DESIGN OF HIGH FREQUENCY CMOS FRACTIONAL-N FREQUENCY DIVIDER

This paper discussed the circuit level design and simulation of fractional-N frequency divider, a circuit block used mainly in frequency synthesizer. The design was done in schematic level. A low power 0.5 micron CMOS technology called CMOSIS5 used for modeling the circuit devices. The frequency divider was design for 900 MHz GSM standard mobile communication application. For the simulation, circuit level simulator SPICE was used. The circuit was run under 1 GHz input frequency. Simulation results show that the circuit was running well in this frequency input.
Toward a Halo Mass Function for Precision Cosmology: The Limits of Universality

We measure the mass function of dark matter halos in a large set of collisionless cosmological simulations of flat ΛCDM cosmology and investigate its evolution at z≲ 2. Halos are identified as isolated density peaks, and their masses are measured within a series of radii enclosing specific overdensities. We argue that these spherical overdensity masses are more directly linked to cluster observables than masses measured using the friends-of-friends algorithm (FOF), and are therefore preferable for accurate forecasts of halo abundances. Our simulation set allows us to calibrate the mass function at z = 0 for virial masses in the range 1011 h−1 M☉ ⩽ M⩽ 1015 h−1 M☉ to ≲5%, improving on previous results by a factor of 2-3. We derive fitting functions for the halo mass function in this mass range for a wide range of overdensities, both at z = 0 and earlier epochs. Earlier studies have sought to calibrate a universal mass function, in the sense that the same functional form and parameters can be used for different cosmologies and redshifts when expressed in appropriate variables. In addition to our fitting formulae, our main finding is that the mass function cannot be represented by a universal function at this level or accuracy. The amplitude of the “universal” function decreases monotonically by ≈20%-50%, depending on the mass definition, from z = 0 to 2.5. We also find evidence for redshift evolution in the overall shape of the mass function.
A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems.

A spectrophotometric method for the measurement of inorganic phosphate (P(i)) has been developed by using 2-amino-6-mercapto-7-methylpurine ribonucleoside and purine-nucleoside phosphorylase (purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1). This substrate gives an absorbance increase at 360 nm on phosphorolysis at pH 6.5-8.5, and at pH 7.6 the change in extinction coefficient is 11,000 M-1.cm-1. The Michaelis-Menten constants of the two substrates with the enzyme are 70 microM for the nucleoside and 26 microM for P(i); the kcat is 40 s-1 (25 degrees C). The assay was shown to quantitate P(i) in solution at concentrations at least down to 2 microM. It can be used to measure the kinetics of P(i) release from phosphatases, such as GTPases and ATPases, by coupling the two enzymic reactions. The utility of this assay was shown by three test systems: glycerol kinase plus D-glyceraldehyde acting as an ATPase and actin-activated myosin ATPase, and myosin subfragment 1, hydrolyzing a single turnover of ATP, releasing P(i) with a rate constant the same as the steady-state ATPase activity.
Syskill & Webert: Identifying Interesting Web Sites

We describe Syskill & Webert, a software agent that learns to rate pages on the World Wide Web (WWW), deciding what pages might interest a user. The user rates explored pages on a three point scale, and Syskill & Webert learns a user profile by analyzing the information on each page. The user profile can be used in two ways. First, it can be used to suggest which links a user would be interested in exploring. Second, it can be used to construct a LYCOS query to find pages that would interest a user. We compare six different algorithms from machine learning and information retrieval on this task. We find that the naive Bayesian classifier offers several advantages over other learning algorithms on this task. Furthermore, we find that an initial portion of a web page is sufficient for making predictions on its interestingness substantially reducing the amount of network transmission required to make predictions.
Phosphatidylinositol 4-Kinase Activation Is an Early Response to Salicylic Acid in Arabidopsis Suspension Cells1[W]

Salicylic acid (SA) has a central role in defense against pathogen attack. In addition, its role in such diverse processes as germination, flowering, senescence, and thermotolerance acquisition has been documented. However, little is known about the early signaling events triggered by SA. Using Arabidopsis (Arabidopsis thaliana) suspension cells as a model, it was possible to show by in vivo metabolic phospholipid labeling with 33Pi that SA addition induced a rapid and early (in few minutes) decrease in a pool of phosphatidylinositol (PI). This decrease paralleled an increase in PI 4-phosphate and PI 4,5-bisphosphate. These changes could be inhibited by two different inhibitors of type III PI 4-kinases, phenylarsine oxide and 30 μm wortmannin; no inhibitory effect was seen with 1 μm wortmannin, a concentration inhibiting PI 3-kinases but not PI 4-kinases. We therefore undertook a study of the effects of wortmannin on SA-responsive transcriptomes. Using the Complete Arabidopsis Transcriptome MicroArray chip, we could identify 774 genes differentially expressed upon SA treatment. Strikingly, among these genes, the response to SA of 112 of them was inhibited by 30 μm wortmannin, but not by 1 μm wortmannin.
Hole detection and boundary recognition in wireless sensor networks

Coverage holes may exist in wireless sensor networks (WSNs) due to presence of obstacles or invalid sensor nodes in the sensing field. Normally, the holes make the data routing failure when the nodes transmit their data back to the sink. In this paper, distributed protocols are developed to identify the boundary nodes surrounding the holes of the sensing filed in WSNs without using any location information. Experimental results demonstrate that our algorithm can precisely and correctly identify the boundary nodes even in sparsely sensors deployed regions. Besides, our algorithm can give better performance in terms of control packet overhead and simulation time as compared to previous work.
Extracting geometric information from images with the novel Self Affine Feature Transform

Based on our research, the Self Affine Feature Transform (SAFT) was introduced as it extracts quantities which hold information of the edges in the investigated image region. This paper gives details on algorithms which extract various geometric information from the SAFT matrix. As different image types should be analysed differently, a classification procedure must be performed first. The main contribution of this paper is to describe this classification in details. Information extraction is applied for solving different 2-dimensional image processing tasks, amongst them the detection of con­ver­gent lines, circles, ellipses, parabolae and hiperbolae or localizing corners of calibration grids in a robust and accurate manner.
Attention without awareness in blindsight

The act of attending has frequently been equated with visual awareness. We examined this relationship in ‘blindsight’: a condition in which the latter is absent or diminished as a result of damage to the primary visual cortex. Spatially selective visual attention is demonstrated when information that stimuli are likely to appear at a specific location enhances the speed or accuracy of detection of stimuli subsequently presented at that location. In a blindsight subject, we showed that attention can confer an advantage in processing stimuli presented at an attended location, without those stimuli entering consciousness. Attention could be directed both by symbolic cues in the subject's spared field of vision or cues presented in his blind field. Cues in his blind field were even effective in directing his attention to a second location remote from that at which the cue was presented. These indirect cues were effective whether or not they themselves elicited non–visual awareness. We concluded that the spatial selection of information by an attentional mechanism and its entry into conscious experience cannot be one and the same process.
Complete nucleotide sequence, genome organization, and biological properties of human immunodeficiency virus type 1 in vivo: evidence for limited defectiveness and complementation

Previous studies of the genetic and biologic characteristics of human immunodeficiency virus type 1 (HIV-1) have by necessity used tissue culture-derived virus. We recently reported the molecular cloning of four full-length HIV-1 genomes directly from uncultured human brain tissue (Y. Li, J. C. Kappes, J. A. Conway, R. W. Price, G. M. Shaw, and B. H. Hahn, J. Virol. 65:3973-3985, 1991). In this report, we describe the biologic properties of these four clones and the complete nucleotide sequences and genome organization of two of them. Clones HIV-1YU-2 and HIV-1YU-10 were 9,174 and 9,176 nucleotides in length, differed by 0.26% in nucleotide sequence, and except for a frameshift mutation in the pol gene in HIV-1YU-10, contained open reading frames corresponding to 5'-gag-pol-vif-vpr-tat-rev-vpu-env-nef-3' flanked by long terminal repeats. HIV-1YU-2 was fully replication competent, while HIV-1YU-10 and two other clones, HIV-1YU-21 and HIV-1YU-32, were defective. All three defective clones, however, when transfected into Cos-1 cells in any pairwise combination, yielded virions that were replication competent and transmissible by cell-free passage. The cellular host range of HIV-1YU-2 was strictly limited to primary T lymphocytes and monocyte-macrophages, a property conferred by its external envelope glycoprotein. Phylogenetic analyses of HIV-1YU-2 gene sequences revealed this virus to be a member of the North American/European HIV-1 subgroup, with specific similarity to other monocyte-tropic viruses in its V3 envelope amino acid sequence. These results indicate that HIV-1 infection of brain is characterized by the persistence of mixtures of fully competent, minimally defective, and more substantially altered viral forms and that complementation among them is readily attainable. In addition, the limited degree of genotypic heterogeneity observed among HIV-1YU and other brain-derived viruses and their preferential tropism for monocyte-macrophages suggest that viral replication within the central nervous system may differ from that within the peripheral lymphoid compartment in significant and clinically important ways. The availability of genetically and biologically well characterized HIV-1 clones from uncultured human tissue should facilitate future studies of virus-cell interactions relevant to viral pathogenesis and drug and vaccine development.
Fossiliferous Localities of the Nachola-Samburu Hills Area, Northern Kenya

In the four geographic/stratigraphic areas of the Samburu Hills and Nachola. west of Baragoi, Kenya. a significant number of fossiliferous localities was found. Nachola area is dated to the middle Miocene, the Namurungule Formation in Samburu Hills to the upper Miocene, Kongia area (0 the Mio-Pliocene and Holocene to the area near Suguta Valley and in the drainage systems of the Samburu Hills to the Holocene. The site BG X in Nachola yielded a number of fossils provisionally assigned to Kenyapitlzecus. An important large hominoid specimen occurred in Site SH n of the Namurungule Fonnation. Undoubtedly a great many additional sites await discovery.
Short and Long Term Effect of Caffeine on Liver, Kidney as well as Glucose, Insulin, Triglycerides and Cholesterol on Normal Rats.

2 Abstract: The present study investigated the long and short term effect of caffeine on some blood parameters in rats. In short term the rats administered caffeine at either (10, 40, 160 mg/kg body weight) for 1 month. In long term the caffeine was administered orally each day at either (5, 20, 80 mg/kg body weight) for 2 months and all analysis of long term were done after one and two months of treatment. The levels of glucose insulin, urea, creatinin, uric acid, ALT, AST, albumin, total protein, globulin, albumin/globulin ratio, total cholesterol and triglycerides were determined in serum of these rats. The results showed that there is no significant differences between control and groups given caffeine in both short and long term except in the case of glucose, there is a significant reduction in glucose level at 5, 20 and 80 mg/kg body weight/day (after 2 months of the long term), and 160 mg/kg body weight/day (short term) caffeine in the treated groups. It was observed that there is a significant reduction in insulin level at 80 mg caffeine/kg body weight/day in the treated group (after 2 months). The concentration of urea was increased after treatment at 5 and 20 mg caffeine/kg body weight/day. The results showed that low dose of caffeine did not affect on blood parameters in both short and long term, but the high dose (80 mg caffeine/kg body weight/day) decreased serum glucose and insulin levels.