Miracle-dz/UniFAR-FTUs huggingface dataset:
The neuropharmacology of sleep and wakefulness.

Attempts to understand the physiology of sleep and wakefulness have been gov­ erned, on the one hand, by the specific phenomena that the investigator has chosen to explain, and, on the other, by the concepts 1Uld techniques available for studying the central nervous system. Prior to the discovery of rapid eye movement (REM) sleep in 1953, and its association with dreaming, investigators had only to explain sleep and wakefulness and the oscillation between the two states. Thus, investigators of "wet" physiology looked for "hypnotoxins" which accumulated during wakeful­ ness and which were presumably dissipated during sleep (1). Similarly, investigators of "dry" physiology explained sleep as a passive state resulting from inactivity of the reticular activating system (2). The discovery that consciousness consists of three major states (REM, wakeful­ ness, and nonREM) complicated but not not obviate these older approaches. It became necessary, however, to account not only for the physiology of each state, but also for their orderly sequence (that is, sleep normally begins with the nonREM phase and consists of the well-known nonREM-REM cycle). Thus, more recent biochemical models, such as that of Jouvet (2), postulates that the mechanism re! iponsible for nonREM sleep "primes" and "triggers" REM sleep. Similarly', the neurophysiological model of Hobson & McCarley (3) suggests that nonREM and REM sleep result from the reciprocal interaction of two anatomically distinct neuronal groups. Physiological models that account for this normal, orderly se­ quence (wakefulness � nonREM � REM) must be flexible enough, however, to account ultimately for the expected deviation (wakefulness � REM � nonREM) which is seen in certain pathological conditions (narcolepsy, psychotic depression), following REM sleep deprivation, and in "phase shift" studies.
Acute Intermittent Porphyria: Novel Etiologic and Pathogenic Therapies Based on RNA Transfer to the Liver

Acute Intermittent Porhyria (AIP) is an inherited autosomal dominant disorder resulting from deficient porphobilinogen deaminase (PBGD) catalytic activity due to heterozygous mutations of HMBS gene, the third enzyme of the heme biosynthetic pathway. Heme is the prosthetic group of many critical hemoproteins. ALAS1, the first and rate-limiting enzyme of heme biosynthesis, is negatively regulated by heme stores. (1) In AIP patients PBGD haploinsufficiency reduces heme availability under conditions of increased heme demands leading to ALAS1 upregulation and increased production and accumulation of porphobilinogen (PBG) and of aminolevulinic acid (ALA), a neurotoxic metabolite. (1) Symptomatic AIP is characterized by the occurrence of acute neurovisceral attacks which can be sporadic or recurrent. During these episodes the levels of ALA and PBG increase further and this is accompanied by diffuse abdominal pain, vomiting, tachycardia and hypertension. This article is protected by copyright. All rights reserved.
Separations of Matroid Freeness Properties

Properties of Boolean functions on the hypercube invariant with respect to linear transformations of the domain are among the most well-studied properties in the context of property testing. In this paper, we study the fundamental class of linear-invariant properties called matroid freeness properties. These properties have been conjectured to essentially coincide with all testable linear-invariant properties, and a recent sequence of works has established testability for increasingly larger subclasses. One question left open, however, is whether the infinitely many syntactically different properties recently shown testable in fact correspond to new, semantically distinct ones. This is a crucial issue since it has also been shown that there exist subclasses of these properties for which an infinite set of syntactically different representations collapse into one of a small, finite set of properties, all previously known to be testable. An important question is therefore to understand the semantics of matroid freeness properties, and in particular when two syntactically different properties are truly distinct. We shed light on this problem by developing a method for determining the relation between two matroid freeness properties P and Q. Furthermore, we show that there is a natural subclass of matroid freeness properties such that for any two properties P and Q from this subclass, a strong dichotomy must hold: either P is contained in Q or the two properties are "well separated. " As an application of this method, we exhibit new, infinite hierarchies of testable matroid freeness properties such that at each level of the hierarchy, there are functions that are far from all functions lying in lower levels of the hierarchy. Our key technical tool is an apparently new notion of maps between linear matroids, called matroid homomorphisms, that might be of independent interest.
Deformation of coracoacromial ligament during overhead movement as an early indicator of subacromial impingement in elite adolescent badminton players

ABSTRACT Objectives: Deformation of the coracoacromial ligament during overhead movement has been linked to shoulder pathologies such as impingement and rotator cuff tear. We, therefore, explored this relationship in a group of elite adolescent badminton players. Method: We performed bilateral shoulder physical and ultrasonographic examination in 35 adolescent asymptomatic badminton players, 13 players with unilateral shoulder pain, and 15 non-athletes of similar age. Coracoacromial ligament deformation, defined as the maximal vertical distance between the ligament apex to a line connecting the acromion and coracoid process, was measured during shoulder abduction and internal rotation and compared within and between groups. Other ultrasonographic measurements and the incidence of shoulder pathologies were also evaluated. Result: Among badminton athletes who reported dominant shoulder pain, coracoacromial ligament deformation was significantly larger in their dominant shoulder than in their non-dominant shoulder (3.5 and 2.0 mm, respectively; p = 0.013); this difference was not present in other groups. Regardless of the presence or absence of pain, athletes displayed more coracoacromial ligament deformation and increased supraspinatus tendon thickness in their dominant shoulder than did the control group. Abnormal ultrasound findings were noted in all groups; however, the incidence was not significantly different. Conclusion: Increased coracoacromial ligament deformation during overhead movement is associated with shoulder pain in elite adolescent badminton players. Our findings may help clinicians identify athletes at risk of subacromial impingement syndrome.
Under Consideration for Publication in Theory and Practice of Logic Programming Deriving a Fast Inverse of the Generalized Cantor N-tupling Bijection

We attack an interesting open problem (an efficient algorithm to invert the generalized Cantor N-tupling bijection) and solve it through a sequence of equivalence preserving transformations of logic programs, that take advantage of unique strengths of this programming paradigm. An extension to set and multiset tuple encodings, as well as a simple application to a " fair-search " mechanism illustrate practical uses of our algorithms. The code in the paper (a literate Prolog program, tested with SWI-Prolog and Lean Prolog) is available at
Differential Genetic Particle Swarm Optimization for Continuous Function Optimization

In this paper, to introduce consistency and diversity, the concept of inertia weight is introduced to a modified genetic particle swarm optimization which was derived from the genetic particle swarm optimization (GPSO) and the differential evolution (DE). The proposed differential genetic particle swarm optimization (DGPSO) is implemented to thirteen well-known constrained optimization functions. And the simulation results have shown the feasibility and effectiveness. Moreover, DGPSO is employed to solve a tension/compression string design problem, and by comparison with the other methods, DGPSO has provided better results.
Scaling of parallel multiple sequence alignment on the supercomputer JUQUEEN

In this paper is proposed optimization, scaling, performance evaluation and profiling of parallel multiple sequence alignment based on ClustalW algorithm on the supercomputer BlueGene/Q, so-called JUQUEEN, for the case study of the influenza virus sequences. For this purpose a parallel I/O interface for simultaneous and independent access to single file collectively has been designed and verified on the basis of parallel program implementation on the supercomputer JUQUEEN.
Immunoprotective Activity and Safety of a RespiratorySyncytial Virus Vaccine: Mucosal Delivery of Fusion Glycoprotein with aCpG OligodeoxynucleotideAdjuvant

ABSTRACT CpG oligodeoxynucleotides (ODN) were identified that stimulated immunoglobulin production and cell proliferation in cotton rat cells in vitro. Three of these ODN were used as a mucosal adjuvant in the noses of cotton rats immunized via this route with respiratory syncytial virus fusion (F) protein. The CpG ODN markedly increased the cotton rat humoral neutralizing-antibody response to respiratory syncytial virus. Such immunized animals had a marked reduction in the production of infectious virus after a live-virus challenge. Animals immunized with the combination of F protein and CpG developed enhanced pulmonary pathology consisting of alveolitis and interstitial pneumonitis after a live-virus challenge. Similar enhanced disease has been seen in cotton rats and children immunized with formalin-inactivated respiratory syncytial virus.
Empirical null distribution-based modeling of multi-class differential gene expression detection

In this paper, we study the multi-class differential gene expression detection for microarray data. We propose a likelihood-based approach to estimating an empirical null distribution to incorporate gene interactions and provide a more accurate false-positive control than the commonly used permutation or theoretical null distribution-based approach. We propose to rank important genes by p-values or local false discovery rate based on the estimated empirical null distribution. Through simulations and application to lung transplant microarray data, we illustrate the competitive performance of the proposed method.
Crystal structure of diaqua[5,10,15,20-tetrakis(4-bromophenyl)porphyrinato-κ4 N]magnesium

The title compound, [Mg(C44H24Br4N4)(H2O)2] or [Mg(TBrPP)(H2O)2], where TBrPP is the 5,10,15,20-tetrakis(4-bromophenyl)porphyrinato ligand, was obtained unintentionally as a by-product of the reaction of the [Mg(TBrPP)] complex with an excess of dimethylglyoxime in dichloromethane. The entire molecule exhibits point group symmetry 4/m. In the asymmetric unit, except for two C atoms of the phenyl ring, all other atoms lie on special positions. The MgII atom is situated at a site with symmetry 4/m, while the N and the C atoms of the porphyrin macrocycle, as well as two C atoms of the phenyl ring and the Br atom lie in the mirror plane containing the porphyrin core. The H atoms of the axially bonded water molecule are incompatible with the fourfold rotation axis and are disordered over two sites. In the crystal, molecules are packed in rows along [001]. Weak intermolecular C—H⋯π and C—H⋯Br interactions, as well as O—H⋯Br hydrogen bonds, stabilize the crystal packing.
Prostate cancer early detection

Because guidelines for the early detection of prostate cancer were developed by the ACS in the early 1990s, many variants of the total PSA assay have been introduced in attempts to increase the sensitivity of screening programs (cancer detection) while maintaining their specificity (elimination of unnecessary biopsies). Again, it is important to note that the NCCN guidelines recommend a method by which individuals and their physicians can use these new methods rationally for the early detection of prostate cancer. These guidelines are not designed to provide an argument for the use of early detection programs for prostate cancer. Rather, they are meant to provide a vehicle by which early detection efforts can be practiced in an evidence-based, systematic fashion in patients who choose to participate in such programs. The NCCN guidelines incorporate many new validated findings in addition to the DRE and PSA test. These new factors include percent-free PSA, PSA velocity, PSA testing intervals, biopsy pathology, and TRUS-guided biopsy techniques. The panel will re-examine the clinical utility of these new modalities annually and the guidelines will be modified accordingly. In addition, future iterations of these guidelines may incorporate new serum markers currently undergoing clinical investigation. It is the hope of the NCCN and this guideline panel that these algorithms will achieve the goal of assisting patients and clinicians who are choosing a program of early detection for prostate cancer to make decisions regarding the need for prostate biopsy. Any clinician who uses these guidelines is expected to exercise independent medical judgment in the context of the individual clinical circumstances to determine the patient's need for prostate biopsy. These guidelines will continue to evolve as the field of prostate cancer advances.
PiSite: a database of protein interaction sites using multiple binding states in the PDB

The vast accumulation of protein structural data has now facilitated the observation of many different complexes in the PDB for the same protein. Therefore, a single protein complex is not sufficient to identify their interaction sites, especially for proteins with multiple binding states or different partners, such as hub proteins. PiSite is a database that provides protein–protein interaction sites at the residue level with consideration of multiple complexes at the same time, by mapping the binding sites of all complexes containing the same protein in the PDB. PiSite provides easy web interfaces with an interactive viewer working with typical web browsers, and the different binding modes can be checked visually. All of the information can also be downloaded for further analyses. In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein–protein interfaces. PiSite is available at http://pisite.hgc. jp
Evaluation of TCP Performance Using NDG Loss Predictor in Wireless Networks

Transmission control protocol (TCP), a widely used transport layer protocol provides reliable service and end-to-end congestion control. Performance of TCP is satisfactory in wired networks but fails to perform well in wireless networks. It is because in wireless networks two types of packet losses are important. Congestion loss and transmission loss. Transmission loss can be ignored in wired networks whereas very frequent in wireless networks. Transmission loss is due to random bit error rate (BER). If the packet loss is due to congestion, TCP should react such that it minimises the congestion in the network. If the loss is due to transmission, TCP should continue with its operations. Suppose, a congestion loss is incorrectly classified as transmission loss, the sources will not decrease their sending rate and congestion will build up in the networks causing reduction in the throughput. Similarly, if transmission loss is treated as a congestion loss, the sources will unnecessarily reduce its offered load causing reduction in the throughput. Thus, the impact of such misclassification is considered to be most significant in maintaining the quality of service (QoS) in the wireless networks. To satisfy these challenges, we propose a model based scheme to adopt sending rate to the losses due to congestion and BER. The model distinguishes congestion loss from transmission loss using the scheme proposed in [8], [9]. If the packet loss is due to congestion (Beta = 0), congestion control mechanism is being invoked. If the packet loss is due to transmission (Beta = 0:1), fast-recovery is being used to gain the loss caused by BER and TCP continues its operation. This helps in achieving good throughput in wireless networks. Using this model, we analyse (i) round trip time (RTT), congestion window (cwnd) dynamics, instantaneous queue length at the bottleneck link, the mechanism of packet dropping, and packet loss (ii) delay-RTT, delay-queue (iii) fast recovery of cwnd, and (iv) the throughput. The experimental results show good performance of TCP over the wireless network in presence of BER.
CSE 280 Class Projects ( Suggested ) Vineet Bafna January 22 , 2008 Projects 1 Population history

To do this, people usually study mtDNA (or the Y chromosomes). The reason is simple: unlike in the autosomal chromosomes, there is no recombination, implying that each DNA sequence has a unique parent. If it were also true that there were no recurrent mutations, known efficient algorithms for character based phylogenies could reconstruct the tree uniquely. Recurrent mutations could make the problem harder, but not insurmountable. However, as more individuals are genotyped, the complexity of these algorithms will grow. Complete mtDNA of over 1500 humans is available. (EX:http://www.bch.umontreal.ca/ogmp/projects/other/mt list.html).
Experimental evaluation of simplified verification methods for responsive communication protocols

We consider responsiveness verification of communication protocols on the client-server system CS/sub N/, which consists of one client site and N (N/spl ges/2) server sites, under the assumption that a single transient failure occurs on any one server site. For the verification, a typical naive method NAIV generates exhaustively all abnormal system states reachable after the failure, and then calculates the recovery time needed for returning to a normal state. We propose two simplified methods (RSY M and EST) to reduce the overheads needed for the method NAIV. The first method (RSY M) takes notice of symmetric properties on the system CS/sub N/ and considers the case where a single transient failure occurs on a specific server site. The second method (EST) verifies the responsiveness on the restricted system CS/sub 2/, and then estimates from its result the responsiveness on the system CS/sub N/. Then we perform simulation experiments to evaluate the proposed methods. The experimental results show that: the first method RSY M can reduce the overheads of the method NAIV, while keeping accuracy in evaluating the recovery time; and the second method EST succeeds in both reducing further the overheads of the method RSY M and assuring good approximation for the recovery time.
Extraction of Linked Data Triples from Japanese Wikipedia Text of Ukiyo-e Painters

DBpedia provides Linked Data extracted from info boxes in Wikipedia articles. Extraction is easier from an infobox than from text because an info box has a fixed-format table to represent structured information. To provide more Linked Data, we propose a method for Linked Data triple extraction from Wikipedia text. In this study, we conducted an experiment to extract Linked Data triples from Wikipedia text of ukiyo-e painters and achieved precision of 0.605.
Does Na+ really play a role in Ca2+ homeostasis in hypertension?

contraction is a cellular event directly modulated by the cytoplasmic concentration of Ca2+, which binds to calmodulin, leading to the activation of myosin light chain kinase. The use of Ca2+ for intracellular signaling implies a tight local and global control of its cytoplasmic concentration and
The Mercury System: Embedding Computation into Disk Drives

Abstract : Having inexpensive data storage has enabled the amassing of vast amounts of information. At present, these data sets far exceed the capacity of modern processors, so searching them has become a serious challenge. In a recent invited talk at the High Performance Embedded Computing Workshop, John Reynders of Celera Genomics commented that, "The size of the databases we deal with is no longer measured in terabytes, but in exabytes. " The Mercury system is a prototype data search engine that can be embedded within the disk drive itself. We focus on the specific problems associated with searches of unstructured, unindexed data. Three specific applications include approximate matching of text (important for text searches of specific interest to homeland security where the original alphabet is different than the Latin alphabet and transliteration is involved), genomics and proteomics searches (important biological applications), and image searches (also of significant interest for homeland security).
SKRINING PLASMA NUTFAH PADI TERHADAP CEKAMAN KEKERINGAN

Rice germplasm is a source of genetic traits in the development of high yielding varieties of rice. This study aims to obtain drought tolerant trait of rice germplasm so that it could be used as a donor in the development of drought tolerant rice. The experiment was conducted from April to September 2010 in the Experimental Site of Indonesian Agriculture Environment Research Institute, Jakenan, Pati, Jawa Tengah using Randomized Block Design (RBD) with three replications. The material used is 64 accessions of rice germplasm and 6 varieties of checks. The result showed that the character of maturity age and the number of filled grain per panicle have posi- tive correlation with grain yield per plant. Four accessions namely, Pelempung Jambi, Padi Jarum Emas, Padi Kuning, Cempo Abang Ner and Botel, have been selected tolerant to drought stress and high yielding based on the character of grain yield per plant, maturity age, and the number of filled grain per panicle. Based on rolling and drying leaf on heading phase, the fifth accessions have tolerance to drought stress with score 1–5. Fifth accession can be used as donor on development of drought tolerant rice.
Cell-based screens and phenomics with fission yeast

Abstract Next-generation sequencing approaches have considerably advanced our understanding of genome function and regulation. However, the knowledge of gene function and complex cellular processes remains a challenge and bottleneck in biological research. Phenomics is a rapidly emerging area, which seeks to rigorously characterize all phenotypes associated with genes or gene variants. Such high-throughput phenotyping under different conditions can be a potent approach toward gene function. The fission yeast Schizosaccharomyces pombe (S. pombe) is a proven eukaryotic model organism that is increasingly used for genomewide screens and phenomic assays. In this review, we highlight current large-scale, cell-based approaches used with S. pombe, including computational colony-growth measurements, genetic interaction screens, parallel profiling using barcodes, microscopy-based cell profiling, metabolomic methods and transposon mutagenesis. These diverse methods are starting to offer rich insights into the relationship between genotypes and phenotypes.