Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of Rab GDP-Dissociation Inhibitor in Complex with Prenylated YPT1 GTPase

Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells whose function is governed by the guanosine diphosphate (GDP) dissociation inhibitor (RabGDI). Using a combination of chemical synthesis and protein engineering, we generated and crystallized the monoprenylated Ypt1:RabGDI complex. The structure of the complex was solved to 1.5 angstrom resolution and provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins. Isoprenoid binding requires a conformational change that opens a cavity in the hydrophobic core of its domain II. Analysis of the structure provides a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.
Cloning, expression and sequencing of Helicobacter felis urease genes

Urease genes from Helicobacter felis were cloned and expressed in Escherichia coli cells. A genomic bank of Sau3A‐digested H. felis chromosomal DNA was created using a cosmid vector. Cosmid clones were screened for urease activity following subculture on a nitrogen‐limiting medium. Subcloning of DNA from an urease‐positive cosmid cione led to the construction of plLL205 (9.5 kb) which conferred a urease activity of 1.2±0.5 μmole urea min‐1 mg‐1 bacterial protein to E. coli HB101 bacteria grown on a nitrogen‐limiting medium. Random mutagenesis using a MiniTn3‐Km transposable element permitted the identification of three DNA regions on plLL205 which were necessary for the expression of an urease‐positive phenotype in E. coii clones. To localize the putative structural genes of H. felis on plLL205, extracts of clones harbouring the mutated copies of the plasmid were analysed by Western blotting with anti‐H. felis rabbit serum. One mutant cione did not synthesize the putative UreB subunit of H. felis urease and it was postulated that the transposable element had disrupted the corresponding structural gene. By sequencing the DNA region adjacent to the transposon insertion site two open reading frames, designated ureA and ureB, were identified. The polypeptides encoded by these genes had caicuiated moiecuiar masses of 26 074 and 61 663 Da, respectively, and shared 73.5% and 88.2% identity with the corresponding gene products of Helicobacter pylori urease.
Epidural anesthesia and analgesia: implications for perioperative coagulability.

pidural gained E in Dart anesthesia and analgesia (EAA) has in popularity during the last 20 yr (1-3), because evidence has accumulated to support numerous physiologic benefits and superior pain relief. Whether combined general/epidural anesthesia with epidural analgesia continued into the postoperative period results in significant differences in outcome compared with general anesthesia alone remains controversial (4-6). The debate is in need of more and better data to support the opposing position. The study by Tuman et al. in this issue is welcome for it provides new evidence regarding the possible mechanism of the purported beneficial effects of EAA on postoperative morbidity in patients undergoing peripheral vascular surgery. The concept of combining inhalational anesthesia and local infiltration with cocaine to block the nerve paths between the brain and the field of operation was described by Crile in 1910 (8). He coined the word "anoci-association," whereby combined inhalational and local anesthesia excludes the nervous system from all stimulation and perception of pain. Crile noted that for "fair-risk" patients anociassociation was not necessary; however, he suggested that the beneficial state of anoci-association in "handicapped" patients might be vitally important. In 1936, Odom administered epidural anesthesia in a series of 285 patients (9). He reported advantages of profound sensory anesthesia in patients thought to represent a poor operative risk. Odom concluded that epidural anesthesia could be used with safety in patients at increased risk for general anesthesia. Users of perioperative EAA claim numerous beneficial effects resulting in improved outcome in specific patient populations. These effects include the following: amelioration of the neuroendocrine stress response to surgery (10); minimization of protein catabolism (11); improvement in pulmonary function
Comparison of human papillomavirus genotyping using commercial assays based on PCR and reverse hybridization methods

Different tests for human papillomavirus (HPV) screening are commercially available, detecting high‐risk oncogenic HPV types with a pool of genotype‐specific probes. However, it is necessary to establish reliable methods for the identification of individual genotypes. The purpose of this study was to compare three different commercial methods for HPV genotyping: INNO‐LiPA HPV Genotyping v2 (LiPA), Linear Arrays HPV Genotyping Test (LA) and Clinical Arrays Human Papillomavirus (CA). A total of 83 HPV DNA‐positive samples by hybrid capture method were genotyped (82, 78 and 81 by LiPA, LA and CA, respectively). Comparison analysis was limited to the HPV genotypes common to the three assays. There were concordant results (absolute agreement between assays) in 31 samples (39.7%) and compatible results (correspondence for some but not all genotypes) were found in 44 samples (56.4%). Only three samples (3.8%) were considered as discordant (did not show any similarity between the tests). Analyzing kappa values we have a very good agreement (>0.8) for HPV16 and HPV31 and good agreement (0.6–0.8) for HPV types 6, 18, 53 and 66 when all methods are compared. We conclude that all genotyping methods tested are highly comparable and suitable for clinical and epidemiological studies.
Relationship between the renin-angiotensin system genes and diabetic nephropathy in the Chinese.

OBJECTIVE To clarify whether genetic variants of the renin-angiotensin system (RAS) contribute to the development of diabetic nephropathy (DN) in the Chinese. METHODS Totally 173 Chinese subjects of Han nationality from Shanghai were classified into! control, DN (-) and DN (+) groups. The latter was subdivided according to diabetic duration at the onset of DN and the stage of DN. Genotyping of five polymorphic sites in four key genes of the RAS: the AGT-T174M, AGT-M235T and AGTR1 genotypes were determined by PCR/restriction enzyme digestion. The insertion/deletion (I/D) and [ACAC] n-STR microsatellite polymorphic markers were used for ACE and REN genotyping, respectively. Statistical analysis showed comparisons of gene frequencies between any two groups were made with Fisher's exact test or Chi-square test. Logistic regression analysis was performed to identify predictors of DN. RESULTS The frequencies of ACE-DD genotype and ACE-D allele were much higher in DN(+) group than in DN (-) group (0.25 vs 0.05, 0.47 vs 0.29, respectively), so were the frequencies of TT genotype and T allele in AGT-M235T (0.73 vs 0.54, 0.85 vs 0.68, respectively). DN (+) DUR < 5 years group had greatly increased frequencies of AGT-M235T allele and ACE-DD genotype in comparison with DN(-) group (0.92 vs 0.68 and 0.28 vs 0.05, respectively). Logistic regression analysis further identified these two genes as contributing factors to DN. Although AGTR1 and AGT-T174M genotyping analysis revealed differences in frequency distribution between DN (+) and DN (-) or control groups, logistic regression analysis failed to implicate them in the development of DN. CONCLUSIONS Our study revealed RAS genes, ACE and AGT-M235T but not AGT-T174M, AGTR1 or REN genotypes, as contributing factors for DN in type 2 diabetes mellitus in Chinese.
Bmp and Fgf signaling are essential for liver specification in zebrafish

Based on data from in vitro tissue explant and ex vivo cell/bead implantation experiments, Bmp and Fgf signaling have been proposed to regulate hepatic specification. However, genetic evidence for this hypothesis has been lacking. Here, we provide in vivo genetic evidence that Bmp and Fgf signaling are essential for hepatic specification. We utilized transgenic zebrafish that overexpress dominant-negative forms of Bmp or Fgf receptors following heat-shock induction. These transgenes allow one to bypass the early embryonic requirements for Bmp and Fgf signaling, and also to completely block Bmp or Fgf signaling. We found that the expression of hhex and prox1, the earliest liver markers in zebrafish, was severely reduced in the liver region when Bmp or Fgf signaling was blocked just before hepatic specification. However, hhex and prox1 expression in adjacent endodermal and mesodermal tissues appeared unaffected by these manipulations. Additional genetic studies indicate that the endoderm maintains competence for Bmp-mediated hepatogenesis over an extended window of embryonic development. Altogether, these data provide the first genetic evidence that Bmp and Fgf signaling are essential for hepatic specification, and suggest that endodermal cells remain competent to differentiate into hepatocytes for longer than anticipated.
Physiological Function of Alcohol Dehydrogenases and Long-Chain (C30) Fatty Acids in Alcohol Tolerance of Thermoanaerobacter ethanolicus

ABSTRACT A mutant strain (39E H8) of Thermoanaerobacter ethanolicus that displayed high (8% [vol/vol]) ethanol tolerance for growth was developed and characterized in comparison to the wild-type strain (39E), which lacks alcohol tolerance (<1.5% [vol/vol]). The mutant strain, unlike the wild type, lacked primary alcohol dehydrogenase and was able to increase the percentage of transmembrane fatty acids (i.e., long-chain C30 fatty acids) in response to increasing levels of ethanol. The data support the hypothesis that primary alcohol dehydrogenase functions primarily in ethanol consumption, whereas secondary alcohol dehydrogenase functions in ethanol production. These results suggest that improved thermophilic ethanol fermentations at high alcohol levels can be developed by altering both cell membrane composition (e.g., increasing transmembrane fatty acids) and the metabolic machinery (e.g., altering primary alcohol dehydrogenase and lactate dehydrogenase activities).
Cryptanalysis and Improvement of a Block Cipher Based on Multiple Chaotic Systems

Wang and Yu proposed a block cipher scheme based on dynamic sequences generated by multiple chaotic systems, which overcomes the problem of periodical degradation on random sequences due to computational precision. Their scheme has a feature that a plaintext is encrypted by a keystream created from several one-dimensional chaotic maps. However, this feature results in some weaknesses of the encryption algorithm. We show three kinds of attacks in this paper, through which one can recover the plaintext from a given ciphertext without the secret key. We also present an improvement on their scheme, which prevents the three attacks mentioned above. Security of the enhanced cipher is presented and analyzed, which shows that our improved scheme is secure under the current attacks.
Long‐term clinical and Social outcome studies in schizophrenia in relation to the cognitive and emotional side effects of antipsychotic drugs

Evaluation of neuroleptics should include not only the effects on symptoms but also social functioning and the quality of life. Akathisia, cognitive and emotional impairment (cognitive and emotional parkinsonism) are probably the most important reasons for lack of compliance with classical neuroleptics. Atypical neuroleptics such as clozapine and remoxipride offer an advantage because of little impairment of cognitive and emotional functioning. In 122 schizophrenic and schizoaffective therapy‐resistent patients treated with clozapine for up to 17 years, the treatment was stopped in only 8 cases (7%) because of lack of compliance. In patients treated for more than 2 years, 40% were employed and functioned well socially. It is concluded that, in many schizophrenic patients, atypical neuroleptics should be preferred in long‐term maintenance treatment because of a low incidence of extrapyramidal syndromes as well as cognitive and emotional parkinsonism. An “awakening” is often seen when changing from a classical neuroleptic to an atypical one.
Extracellular adenosine production by ecto-5'-nucleotidase protects during murine hepatic ischemic preconditioning.

BACKGROUND & AIMS The liver tolerates ischemia/reperfusion (IR) poorly. The discovery of ischemic preconditioning (IP) has raised hopes that natural pathways could be activated to increase hepatic resistance to ischemia. However, mechanisms of hepatic IP remain largely unknown. Extracellular adenosine has been implicated as an innate anti-inflammatory metabolite, particularly during ischemia. We investigated whether ecto-5'-nucleotidase (CD73), the "pacemaker" enzyme of extracellular adenosine production, is critical for hepatic protection by IP. METHODS Mice were subjected to 4 cycles of portal triad occlusion and reperfusion (3 minutes of ischemia/3 minutes of reperfusion) prior to IR or IR alone. RESULTS Hepatic IP was associated with a significant induction of CD73 transcript and protein. Targeted gene deletion or pharmacologic inhibition of CD73 abolished hepatic protection by IP as measured by lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase serum levels or histologic injury. Increases in extracellular adenosine with IP were significantly attenuated in cd73-deficient (cd73(-/-)) mice. Reconstitution of cd73(-/-) mice with soluble 5'-nucleotidase resulted in complete restoration of hepatoprotection by IP, and hepatic injury following ischemia was attenuated by treatment of WT mice with soluble 5'-nucleotidase. Mice deficient in CD73 did not demonstrate the same degree of IP-dependent inhibition of acute phase complement gene expression/activation as did wild-type mice suggesting that extracellular adenosine attenuates hepatic IR via complement regulation. CONCLUSIONS Extracellular adenosine production by CD73 mediates protection during murine hepatic IP. Use of soluble 5'-nucleotidase may be a potential therapeutic for hepatic ischemia.
DNA testing for more sophisticated clinical management of multiple endocrine neoplasia type 2 (MEN 2)

DNA testing to predict cancer predisposition currently plays an important role in the clinical management of hereditary cancer. MEN 2 syndromes are autosomal dominant inherited cancer syndromes, and DNA testing is now useful in clinical practice of these diseases. MEN 2 syndromes are subclassified into MEN 2A, MEN 2B, and familial medullary thyroid carcinoma (FMTC). MEN 2A is characterized by the development of medullary thyroid carcinoma (MTC), pheochromocytoma and hyperparathyroidism (HPT). MEN 2B is also associated with MTC and pheochromocytoma but has developmental abnormalities such as marfanoid habitus, mucosal neuromas and ganglioneuromatosis. In FMTC, MTC is the only disease feature. Recently,the RETproto-oncogene has been identifiedas the susceptibility gene for MEN 20-3). The gene encodes a receptor tyrosine kinase and its physiological ligands are glial-cell-line-derived neurotropic factor (GDNF) and neurturin (NTN) which require the presence of co-receptors of GDNFR-alpha and NTNR-alpha for signal transduction to occur, respectively (4,5). In MEN 2A and FMTC cases, the mutations are clustered in the extracellular cysteine rich domain (codons 609, 611, 618, 620, 630 and 634) although they were also found in the intracellular tyrosine kinase domain (codons 768, 790, 791, 804 and 891) as rare cases. In the majority of ~N 2B patients, a mutation has been identified at codon 918 in the extracellular tyrosine kinase domain while a mutation at codon 883 was also found in a few cases. Mutational analysis of the RET proto-oncogene cannot only confirm diagnosis of MEN 2 but also identify asymptomatic family members at risk of this syndrome. Before DNA testing was available, both affected and unaffected individuals at 50% risk of MEN 2 were required to undergo annual biochemical screening for MTC, pheochromocytoma and HPT from early childhood. These screening tests include a pentagastrin or combined pentagastrin-ca1cium provocative test which often generated false positive or false negative results in addition to patients' physical discomfort. DNA testing, which is accurate and sensitive and does not give physically adverse effect on patients, has resolved these problems, and has eliminated the need for unnecessary biochemical screening in family members who are not at risk. This diagnostic tool can also allow predisposed family members to have a chance of surgical intervention such as prophylactic thyroidectomy before the development of MTC. Although MTC occurs in over 95% of patients with MEN 2 and is potentially lethal, it can be prevented by prophylactic thyroidectomy. The thyroidectomy is safe when the surgery is performed by an experienced surgeon and thyroid hormone replacement is available. However, it appears controversial to decide when and on which affected family members the prophylactic surgery should be Jpn J Clin OncoI1998;28(10)588-589
The quartz resonator: Electrochemical applications

Since the discovery that the oscillations of resonating quartz crystals can be sustained in a liquid environment, such crystals have quickly found use as a sensitive microbalance in electrochemistry, making possible in situ measurements of mass changes at the electrochemical interface. The early contributions of the IBM Almaden Research Center to this exciting field of development are sketched. The principles of operation are detailed, with emphasis on an intuitive description to permit considerations of new applications. Mass density changes of the order of 10 nanograms per square centimeter (ng/cm2) are routinely detectable as changes in the resonant frequency of about a hertz. The mass density of a monolayer of material ranges from a few tens of ng/cm2 for polymeric materials to a few hundreds of ng/cm2 for metals. Detailed analysis of the electrical behavior of the resonator in liquid media shows that the resonant frequency, the quality factor of the resonance, and the admittance at resonance are all sensitive to the viscoelastic properties of the contacting liquid, having implications in the study of the behavior of non-Newtonian fluids, including polymeric films.
Strategy of storing and accessing small web log files on Hadoop

Hadoop distributed file system(HDFS) was designed to manage large files. For a large number of small files, such as genomic data and web log data, HDFS would suffer from low access and storage efficiency and bring much less benefit. In this paper, we propose an asynchronous merging algorithm based on monitoring the task queue (MTQM) and a prefetching strategy based on Hash index. On the basis of client merging small files, uploading and merging small files can be asynchronous by monitoring the task queue. Meanwhile, small files can be quickly accessed by using prefetching and caching scheme. The experimental results show that the approach proposed in this paper can improve the efficiency of storing and accessing small files and effectively reduce the metadata storage space of NameNode.
Imaging modalities in recurrent head and neck tumors

Patients with recurrent neoplasms of the head and neck present perplexing management problems, and accurate preoperative assessment of their disease is crucial. Thirty-eight patients with suspected recurrent neoplasms comprise this study: 30 had computed tomography scans, 4 had magnetic resonance images, and 4 patients underwent both computed tomography and magnetic resonance imaging to assess the anatomical extent of pathology in 34 malignant and 4 benign tumors. Contrast enhancement was essential for detecting disease on computed tomography scan. Differentiation of recurrent tumor was more difficult when the patient had undergone radiation. Magnetic resonance imaging demonstrated superior visibility in recurrent parotid and paranasal sinus neoplasm, but was less helpful in laryngeal and pharyngeal recurrences. Computed tomography demonstration of a mass with infiltration of normal fat or tissue planes or lymphadenopathy correlated highly with recurrent disease. Imaging techniques and fine points for determining recurrent neoplasms are presented.
L'organisation temporelle de la syllabe dans la parole et dans le chant, étude préliminaire

Dans le chant, l'organisation temporelle de la syllabe est differente de celle qui existe dans la parole et il n'y a pas de tendance a l'isochronisme syllabique L'allongement considerable que subit la syllabe chantee, entraine une modification de l'equilibre voyelle/consonne a l'interieur de la syllabe, ce qui a pour effet d'augmenter la proportion de voyelles et de diminuer la proportion de consonnes. Enfin, les limites d'elasticite des consonnes sont pratiquement identiques dans la parole (16-324 ms) et dans le chant (16-340 ms) en raison de contraintes physiologiques tres puissantes (de type aerodynamique en particulier). Quant aux limites inferieures d'elasticite des voyelles, elles sont egalement tres proches en voix parlee et en voix chantee (respectivement 28 et 40 ms), vraisembla-blement pour des raisons perceptives.
Synchronous CR-OLAP Tool for Efficient Parallel Computing

Real time OLAP , or RTOLAP, is the capability to quickly retrieve, aggregate, analyze and present multidimensional data for cubes whenever there are changes to the data in the relational data sources, without having to run heavy processing on the cube. A big advantage of real time OLAP is that it calculates all relevant data and provides immediate output. One of the main roles of an RTOLAP system is that data is stored directly in main memory, or in an in memory database, enabling quicker access to the data. Another factor affecting the speed of calculation is compression data is compressed, in such a way that it can be accessed must faster in its compressed form. Additionally, pre-calculated values are not stored, therefore avoiding “data explosion”. In contrast to queries for online transaction processing (OLTP) system that typically access only a small portion of a database, OLAP queries may need to aggregate large portion of a database which often leads to performance issues. In this paper introduced CR-OLAP, a cloud based Real Time OLAP system based on a new distributed index structure for OLAP, the distributed PDCR tree, that utilizes a cloud infrastructure consisting of (m+1) multicore processors. With increasing database size, CROLAP dynamically increases m to maintain performance. The distributed PDCR tree data structure supports multiple dimension hierarchies and efficient query processing on the sophisticated dimension hierarchies which are so central to OLAP system. It is particularly efficient for complex OLAP queries that need to aggregate large portions of the data warehouses. The static data cube approach proposed by Gray et.al. and materialize all or a subset of the cuboids of the data cube in order to ensure adequate query performance. Practitioners have called for some time for a real-time OLAP approach where the OLAP system gets updated instantaneously as new data arrives and always provides an up-to-date data warehouse for the decision support process. However, a major problem for real-time OLAP is the significant performance issues with large scale data warehouses. The main aim of our research is to address these problems through the use of efficient parallel computing methods. In this paper proposed a distributed data structure for real time OLAP. To our knowledge, the real-time OLAP system that has been parallelized and optimized for contemporary multi-core architectures allows for multiple insert and multiple query transactions to be executed in parallel and in real-time.