Miracle-dz/UniFAR-FTUs huggingface dataset:
An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor

ABSTRACT During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. IMPORTANCE During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs.
Design of a PIFA-Driven Compact Yagi-Type Pattern Diversity Antenna for Handheld Devices

This letter presents a compact folded-strip printed inverted-F antenna (FS-PIFA) having dipole-like radiation pattern. The designed antenna operates at 2.45-GHz band and offers 5.75% bandwidth. A parametric study of the FS-PIFA is presented to show the effect of symmetry on the quality factor. Next, an FS-PIFA-driven compact Yagi-Uda antenna is designed by using folded strips as passive elements. The dimension of the Yagi antenna is optimized using mutated particle swarm optimization (PSO) algorithm. The designed Yagi-Uda antenna operates in the 2.45-GHz band with front-to-back (F/B) ratio of 17 dB and gain of 4.6 dBi. Finally, a pattern diversity antenna is realized by placing two such Yagi-Uda antennas back to back with a common reflector. The diversity antenna is very compact, and it occupies approximately 41 ×68 ×5 mm3 volume. The port isolation is about 24 dB. The signal envelope correlation coefficient of the diversity antenna is found to be as low as 0.074.
Arabic Continuous Speech Recognition System using Sphinx-4

Speech is the most natural form of human communication and speech processing has been one of the most exciting areas of the signal processing. Speech recognition technology has made it possible for computer to follow human voice commands and understand human languages. The main goal of speech recognition area is to develop techniques and systems for speech input to machine and treat this speech to be used in many applications. As Arabic is one of the most widely spoken languages in the world. Statistics show that it is the first language (mother-tongue) of 206 million native speakers ranked as fourth after Mandarin, Spanish and English. In spite of its importance, research effort on Arabic Automatic Speech Recognition (ASR) is unfortunately still inadequate[7]. This thesis proposes and describes an efficient and effective framework for designing and developing a speaker-independent continuous automatic Arabic speech recognition system based on a phonetically rich and balanced speech corpus. The developing Arabic speech recognition system is based on the Carnegie Mellon university Sphinx tools. To build the system, we develop three basic components. The dictionary which contains all possible phonetic pronunciations of any word in the domain vocabulary. The second one is the language model such a model tries to capture the properties of a sequence of words by means of a probability distribution, and to predict the next word in a speech sequence. The last one is the acoustic model which will be created by taking audio recordings of speech, and their text transcriptions, and using software to create statistical representations of the sounds that make up each word. The system use the rich and balanced database that contains 367 sentences, a total of 14232 words. The phonetic dictionary contains about 23,841 definitions corresponding to the database words. And the language model contains14233 mono-gram and 32813 bi-grams and 37771 tri-grams. The engine uses 3-emmiting states Hidden Markov Models (HMMs) for tri-phone-based acoustic models.
Outcome of liver resection and transplantation for fibrolamellar hepatocellular carcinoma

Abstract Fibrolamellar hepatocellular carcinoma (FL HCC) is an uncommon variant of hepatocellular carcinoma occurring usually in non-cirrhotic livers. Hepatic resection or transplantation offers the only chance of cure. We reviewed our experience of surgery for FL HCC from 1985–1998. Twenty patients with FL HCC (13 females and 7 males) median age 27 years (range 12–69) were treated either by hepatic resection [n = 11; extended right hepatectomy (5), extended left hepatectomy (1), right hemihepatectomy (2), left hemihepatectomy (2), left lateral segmentectomy (1)] or, if the disease was non-resectable, by transplantation (n = 9). The median follow up was 25 months (1–63). The prognostic factors analysed included size [less than 5 cm (3 patients), more than 5 cm (17 patients)], number [solitary (16 patients), multiple (4 patients)], capsular invasion (6 patients), vascular invasion (11 patients) and lymph node invasion (6 patients). The overall survival at 1, 3 and 5 years was 89.5, 75 and 50 %, respectively. The liver resection survival was better than liver transplantation survival at 3 years 100 vs 76 %, respectively (P < 0.025). Although all prognostic factors analysed did not show a significant difference, there is tendency that tumour stage was the most significant for prognosis. Most of the patients in this study are young and presented without specific symptoms, with normal liver function range and had no tumour marker to help in diagnosis. As a result most of our patients were diagnosed late. However the outcome of surgical intervention was favourable.
99mTc-MIBI Imaging in the Presurgical Characterization of Thyroid Follicular Neoplasms: Relationship to Multidrug Resistance Protein Expression

Recently, thyroid 99mTc-methoxyisobutylisonitrile (99mTc-MIBI) scintiscanning has been proposed in an attempt to preoperatively identify thyroid malignancies, but discrepant results have been reported for oncocytic lesions. The aim of this study was to investigate the usefulness of visual and semiquantitative analyses of 99mTc-MIBI scintigraphy for preoperatively characterizing thyroid nodules with indeterminate cytologic diagnoses, segregating in advance nononcocytic variants from those that are oncocytic. This study also aimed to analyze the relationship between 99mTc-MIBI images and P-glycoprotein (P-gp)/multidrug resistance-associated protein-1 (MRP1) immunohistochemical expression. Methods: Fifty-one consecutive patients with cold thyroid nodules cytologically diagnosed as nononcocytic or oncocytic follicular neoplasm were prospectively studied. Visual and semiquantitative 99mTc-MIBI scanning was performed and the diagnoses of the lesions were histologically proven by subsequent thyroidectomy. Immunohistochemical evaluation of P-gp and MRP1 was also performed on surgical samples. Results: Visual and semiquantitative 99mTc-MIBI scintiscans showed a low specificity in preoperatively discriminating malignant oncocytic lesions. In nononcocytic nodules, the semiquantitative method was more accurate than the visual (94.44% and 77.78%, respectively). P-gp protein expression was negative in all thyroid lesions, whereas apical plasma membrane MRP1 expression was found in 78% of the lesions with a negative 99mTc-MIBI retention index, compared with 11% of lesions with a positive retention index, correlating most strongly with a negative 99mTc-MIBI RI in those cases with strong MRP1 apical expression. Conclusion: Semiquantitative 99mTc-MIBI scintigraphy is an adjunctive method to predict preoperatively the malignant behavior of nononcocytic follicular thyroid nodules indeterminate at fine-needle aspiration biopsy, with a potential impact on the definition of their clinical management. Moreover, the good correlation found between immunohistochemical apical expression of MRP1 and the scintigraphic findings supports the 99mTc-MIBI results and provides tissue information on the molecular mechanisms responsible for 99mTc-MIBI images in thyroid lesions.
An Increase in Glutamate Release Follows a Decrease in Gamma Aminobutyric Acid and the Pubertal Increase in Luteinizing Hormone Releasing Hormone Release in Female Rhesus Monkeys

Previously we have shown that release of γ‐aminobutyric acid (GABA) in the stalk‐median eminence (S‐ME) is high in prepubertal monkeys and that a decrease in GABA release triggers the onset of puberty. However, it is still unclear how disinhibition of the luteinizing hormone releasing hormone (LHRH) neuronal system from GABA input is followed (or accompanied) by an increase in stimulatory signals, such as glutamatergic input to LHRH neurons. To clarify the temporal relationship between the reduction of the GABAergic inhibitory signal and the enhancement of the glutamatergic stimulatory signal in the control of LHRH release at the onset of puberty, we conducted two experiments using a push–pull perfusion method. In the first experiment, we measured developmental changes in release of LHRH, GABA, and glutamate in the S‐ME. LHRH levels were very low in prepubertal monkeys, increased to higher levels in early pubertal monkeys, with the highest LHRH levels occurring in mid‐pubertal monkeys. As we previously observed, GABA levels were high in prepubertal monkeys and then decreased in early‐ and mid‐pubertal monkeys. In contrast, glutamate levels were very low in prepubertal monkeys, increased dramatically in early pubertal monkeys, and then slightly decreased in mid‐pubertal monkeys, although mid‐pubertal levels remained much higher than prepubertal levels. In the second experiment, we measured GABA, glutamate and LHRH in the same samples obtained from prepubertal monkeys which were infused with an antisense oligodeoxynucleotide (AS) for glutamic acid decarboxylase (GAD) 67 mRNA into the S‐ME. GAD67 is a catalytic enzyme for GABA synthesis from glutamate, and AS GAD67 mRNA interferes with GAD67 synthesis. Infusion of the AS GAD67 induced a decrease in GABA release, which subsequently resulted in an increase in LHRH release. Surprisingly, glutamate release also increased several hours after the decrease in GABA release, and the increased LHRH release continued. These data are interpreted to mean that a decrease in GABA synthesis by interference with GAD67 synthesis and the reduction of GABA release in the S‐ME trigger an increase in LHRH release, but that a subsequent increase in glutamate release in the S‐ME further contributes to the pubertal increase in LHRH release at the onset of puberty. The data further support our hypothesis that GAD plays an important role in the mechanism of the onset of puberty.
Impact of Irrigation on Larval Density of Stem-Infesting Pests of Cultivated Sunflower in Kansas

Abstract The guild of stem-infesting insect pests of cultivated sunflower, Helianthus annuus L. , within the central Plains is a concern to producers, chiefly due to losses caused by plant lodging from the sunflower stem weevil, Cylindrocopturus adspersus (LeConte) (Coleoptera: Curculionidae), and Dectes texanus texanus LeConte (Coleoptera: Cerambycidae). The incidence of a root boring moth, Pelochrista womonana (Kearfott) (Lepidoptera: Tortricidae), also has increased. Experiments were conducted in Kansas during 2000–2001 to investigate the effect of irrigation timing and intensity on densities of C. adspersus, D. texanus, and P. womonana larvae within cultivated sunflower stalks. Supplemental soil moisture provided by irrigation during the growing season increased both seed yield and oil content, and it reduced insect densities of the sunflower stem weevil and P. womonana in the sunflower stalk. Results showed that ensuring adequate moisture during the growing season can assist in reducing stem-infesting insect densities, revealing an additional advantage of crop irrigation beyond improved sunflower productivity.
Image fitting using arctan for JPEG AC coefficient prediction

We explore predictive coding for the JPEG baseline sequential algorithm in this article. Our objective is to reduce inter-block redundancy of discrete cosine transform (DCT) blocks. We first present an implementation of image interpolation approach and develop a method for predicting AC coefficients of a block in terms of sum of pixels (or dc coefficients) of some surrounding patches. If we use 2-D quadratic polynomials for interpolation over 24 times 24 pixel area, our method derives the same equations, which JPEG developed for reducing blocking artifacts. Next, we show that nonpolynomial functions such as arctan perform better for AC prediction. We develop additional prediction equations considering different configurations of the interpolation area. Finally, we present performance results, which show that for images compressed at the default quality factor of 75, our equations reduce the AC energy of DCT blocks by about 22% and the final code bit size by about 5.5% over the JPEG sequential algorithm. At the quality factor of 90, the code size reduction is 10.8%. We also present an adaptive DC coding method by considering the prediction algorithm of JPEG-LS. It reduces the average JPEG DC residual by over 20% and the DC code bits by 7.75%.
SNP Analysis of Minimally Evolved t(14;18)(q32;q21)-Positive Follicular Lymphomas Reveals a Common Copy-Neutral Loss of Heterozygosity Pattern

Follicular lymphoma (FL) cases with a t(14;18)(q32;q21) and minimal or no additional karyotypic alterations, such as copy number gains and losses and/or chromosomal rearrangements, may exhibit pathologic features and a clinical behavior similar to those with more complex karyotypes. This study sought to investigate whether the copy-neutral loss of heterozygosity (cnLOH) profiles of these minimally evolved t(14;18)(q32;q21)-positive follicular lymphoma (MEV-FL) cases are similar to or different from the majority of FL cases with more karyotypic alterations. Affymetrix SNP 6.0 array analysis was applied to the tumor genomes of 23 MEV-FL biopsy samples to assess for the presence of cnLOH. These cases carried either a single or no chromosomal abnormality in addition to t(14;18)(q32;q21) as determined by karyotyping. We found that, although these MEV-FL cases had simple karyotypes, they showed very similar cnLOH profiles as compared to cytogenetically complex cases. The most frequent regions affected by cnLOH were 1p (17%), 6p (17%), 12q (13%) and 16p (13%). Our study suggests that cnLOH alterations may serve as important contributors to the pathological and clinical manifestations of FL.
Acute abrin poisoning treated with continuous renal replacement therapy and hemoperfusion successfully

Rationale: Abrin is a highly toxic protein obtained from the seeds of Abrus precatorius, but poisoning due to ingestion of A precatorius is extremely rare in China. Patient concerns: A 16-year-old girl, perfectly healthy before, was admitted to the department of gastroenterology owing to intentional ingestion of 10 crushed A precatorius seeds, with multiple episodes of somnolent and anxious mental status, vomiting, abdominal pain, diarrhea, hematochezia, and hematuria. Diagnosis: Acute abrin poisoning. Interventions: We immediately took effective measures including gastric lavage, purgation, gastric acid suppression by proton pump inhibitor (PPI), liver protection, hemostasis, blood volume and electrolytes resuscitation, continuous renal replacement therapy (CRRT), and hemoperfusion (HP). Outcomes: Her unwell mental status was improved to the point at which she became conscious and relaxed. The symptoms of vomiting, abdominal pain, diarrhea, hematochezia, and hematuria disappeared gradually. The girl eventually made an excellent recovery with no complications at her 3-month follow-up. Lessons: The combination of CRRT and HP is an efficient measure in the treatment of abrin poisoning for which there is no specific antidote. This is the first reported case of an abrin poisoning patient successfully treated by CRRT plus HP. Our experience will be useful to other physicians in managing patients of acute abrin poisoning in the future.
Migrant household homeownership outcomes in large Chinese cities - the sustained impact of hukou

Abstract Homeownership by migrant households in large Chinese cities is increasingly evident and sometimes blamed for driving up local housing prices. Hukou reform grants local hukou to migrants in small cities while it allows large cities to set up hukou entry barriers to control migration. This paper explores whether migrant households’ micro-level characteristics and macro-level urban policies relating to hukou reform have any impact on their housing tenure choices. Using data from a 2009 survey of migrant households in six large cities, this study adopts logistic regression models to examine factors influencing labor migrant households’ tenure decisions. We find that household income and head of household hukou type, contribution to pension fund, and enrollment in health insurance all positively predict homeownership. Migrant households are more likely to be found in cities with larger population size. We argue that city entry barriers create new forms of institutional haves and have-nots and new forms of inequality. The sustained impact of previous hukou types suggests inherited inequalities through intergenerational wealth transfer, which calls for targeted welfare policies to mediate.
Phylogenetic analysis of gag genes from 70 international HIV‐1 isolates provides evidence for multiple genotypes

ObjectiveTo determine the extent of genetic variation among internationally collected HIV-1 isolates, to analyse phylogenetic relationships and the geographic distribution of different variants. DesignPhylogenetic comparison of 70 HIV-1 isolates collected in 15 countries on four continents. MethodsTo sequence the complete gag genome of HIV-1 isolates, build multiple sequence alignments and construct phylogenetic trees using distance matrix methods and maximum parsimony algorithms. ResultsPhylogenetic tree analysis identified seven distinct genotypes. The seven genotypes were evident by both distance matrix methods and maximum parsimony analysis, and were strongly supported by bootstrap resampling of the data. The intra-genotypic gag distances averaged 7%, whereas the inter-genotypic distances averaged 14%. The geographic distribution of variants was complex. Some genotypes have apparently migrated to several continents and many areas harbor a mixture of genotypes. Related variants may cluster in certain areas, particularly isolates from a single city collected over a short time. ConclusionsThe genetic variation among HIV-1 isolates is more extensive than previously appreciated. At least seven distinct HIV-1 genotypes can be identified. Diversification, migration and establishment of local, temporal ‘blooms' of particular variants may all occur concomitantly.
Inducible Tumor Necrosis Factor (TNF) Receptor-associated Factor-1 Expression Couples the Canonical to the Non-canonical NF-κB Pathway in TNF Stimulation*

Background: The NF-κB transcription factor mediates the inflammatory response through canonical and non-canonical pathways. Results: TRAF-1 binds and stabilizes NIK by disrupting its association with TRAF2·cIAP2 complex. Conclusion: These integrated computational-experimental studies identify TRAF1·NIK as a feed-forward complex coupling canonical and non-canonical pathways. Significance: These findings provide insight into how cells decode inflammatory signals into distinct genomic responses. The NF-κB transcription factor mediates the inflammatory response through distinct (canonical and non-canonical) signaling pathways. The mechanisms controlling utilization of either of these pathways are largely unknown. Here we observe that TNF stimulation induces delayed NF-κB2/p100 processing and investigate the coupling mechanism. TNF stimulation induces TNF-associated factor-1 (TRAF-1) that directly binds NF-κB-inducing kinase (NIK) and stabilizes it from degradation by disrupting its interaction with TRAF2·cIAP2 ubiquitin ligase complex. We show that TRAF1 depletion prevents TNF-induced NIK stabilization and reduces p52 production. To further examine the interactions of TRAF1 and NIK with NF-κB2/p100 processing, we mathematically modeled TRAF1·NIK as a coupling signaling complex and validated computational inference by siRNA knockdown to show non-canonical pathway activation is dependent not only on TRAF1 induction but also NIK stabilization by forming TRAF1·NIK complex. Thus, these integrated computational-experimental studies of TNF-induced TRAF1 expression identified TRAF1·NIK as a central complex linking canonical and non-canonical pathways by disrupting the TRAF2-cIAP2 ubiquitin ligase complex. This feed-forward kinase pathway is essential for the activation of non-canonical pathway.