Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of Rep-Mediated Adeno-Associated Virus Origin Nicking

ABSTRACT The single-stranded adeno-associated virus type 2 (AAV) genome is flanked by terminal repeats (TRs) that fold back on themselves to form hairpinned structures. During AAV DNA replication, the TRs are nicked by the virus-encoded Rep proteins at the terminal resolution site (trs). This origin function apparently requires three sequence elements, the Rep binding element (RBE), a small palindrome that comprises a single tip of an internal hairpin within the TR (RBE′), and the trs. Previously, we determined the sequences at the trs required for Rep-mediated cleavage and demonstrated that the trs endonuclease reaction occurs in two discrete steps. In the first step, the Rep DNA helicase activity unwinds the TR, thereby extruding a stem-loop structure at thetrs. In the second step, Rep transesterification activity cleaves the trs. Here we investigate the contribution of the RBE and RBE′ during this process. Our data indicate that Rep is tethered to the RBE in a specific orientation duringtrs nicking. This orientation appears to align Rep on the AAV TR, allowing specific nucleotide contacts with the RBE′ and directing nicking to the trs. Accordingly, alterations in the polarity or position of the RBE relative to the trsgreatly inhibit Rep nicking. Substitutions within the RBE′ also reduce Rep specific activity, but to a lesser extent. Interestingly, Rep interactions with the RBE and RBE′ during nicking seem to be functionally distinct. Rep contacts with the RBE appear necessary for both the DNA helicase and trs cleavage steps of the endonuclease reaction. On the other hand, RBE′ contacts seem to be required primarily for TR unwinding and formation of thetrs stem-loop structure, not cleavage. Together, these results suggest a model of Rep interaction with the AAV TR during origin nicking through a tripartite cleavage signal comprised of the RBE, the RBE′, and the trs.
Notice of RetractionCFD computer simulation on thermal comfort research

An Air-conditioned dormitory in winter is used as a model to study indoor airflow and human thermal comfort. This paper uses κ-ε - three-dimensional turbulence model and N-S equation, considers airflow with room shape and obstacles as one, calculates the indoor airflow and heat transfer problems with overall solution, studies indoor air form especially velocity field with numerical simulation. From the numerical simulation results, we can know that the layout of the school dormitory and air supply mode is appropriate, the air velocity and other parameters meet the relevant standards, and conducive to obtain comfortable indoor thermal environment. The results prove that κ-ε - three-dimensional turbulence model is suitable for calculating indoor airflow field, and can be used in other air-conditioned rooms with different structure in winter.
Multi-objective particle swarm optimization of wind turbine directly connected PMSG

Annual yield energy, compact design and cost of active material as permanent magnet (PM) cost are the fundamental design aspects that permanent magnet synchronous generators (PMSGs) designer should consider. The complexity of the electric machine structure is a challenging task, which requires an optimal design approach. The use of intelligent optimization techniques is widely considered as an appropriate tool in this context. This paper adopts Particle Swarm Optimization (PSO) for the design of PMSG, optimizing for three different optimization functions. The optimization is achieved through the lumped element model of the generator. Then aided with finite element method software, the results from the PSO are verified and compared. The results highlighted that each optimization function serves a different purpose.
Variations in the concentration of phytic acid in the blood of the domestic fowl.

chicks 1, 7, 14 and 21 days of age. The effect of reproductive activity on the concentration of phytic acid in the blood was studied in nine pullets that were bled every 3 days from 18 weeks of age until at least 8 days after the laying of the first egg.
Neuropsychological characteristics of the syndrome of mesial temporal lobe epilepsy.

OBJECTIVE To identify the neuropsychological features of the syndrome of mesial temporal lobe epilepsy (MTLE), a surgically remediable epileptic syndrome defined by the presence of hippocampal sclerosis, using a broad and comprehensive neuropsychological test battery. SETTING Epilepsy surgery center. PATIENTS After scalp adn invasive electroencephalographic monitoring, a consecutive series of 107 adults were found to have intractable complex partial seizures of unilateral left (n = 62) or right (n = 45) temporal lobe origin. Patients were included if they were not retarded and had left hemisphere dominance for speech but no magnetic resonance imaging abnormalities other than hipocampal sclerosis. Histopathological analyses of resected hippocamppi showed that 66 patients had hippocampal sclerosis (MTLE+), and 41 did not have evidence of significant hippocampal sclerosis (MTLE-). INTERVENTIONS None. MAIN DEPENDENT MEASURES: A comprehensive battery of neuropsychological tests that included measures of intelligence, academic achievement, language, visuoperceptual or visuospatial function, memory and learning, attention, and problem-solving abilities. RESULTS The syndrome of MTLE was associated with considerable generalized cognitive impairment (in intelligence, academic achievement, language, and visuospatial functions), but not related to adequacy of performances in other selected cognitive domains (attention or concentration, executive functions). Material-specific memory effects were obtained-primarily for verbal memory in association with left-sided MTLE. CONCLUSIONS Distinct neuropsychological features of spared, compromised, and laterality-specific cognitive impairments characterize the syndrome of MTLE. This information needs to be incorporated into formal syndrome criteria.
Adenosine 3',5'-Monophosphate: Inhibition of Complement-Mediated Cell Lysis

An increase in adenosine 3',5'-monophosphate (cyclic AMP) in rat mast cells, achieved by stimulating the cells with prostaglandin E1, by preventing cyclic AMP breakdown with aminophylline, or by adding exogenous dibutyryl cyclic AMP, prevented complement-mediated cytolysis as assessed by both histamine release and vital dye exclusion. Dibutyryl cyclic AMP also suppressed water-induced osmotic lysis.
Dual Transcriptional Control of amfTSBA, Which Regulates the Onset of Cellular Differentiation in Streptomyces griseus

ABSTRACT The amf gene cluster encodes a probable secretion system for a peptidic morphogen, AmfS, which induces aerial mycelium formation in Streptomyces griseus. Here we examined the transcriptional control mechanism for the promoter preceding amfT (PamfT) directing the transcription of the amfTSBA operon. High-resolution S1 analysis mapped a transcriptional start point at 31 nucleotides upstream of the translational start codon of amfT. Low-resolution analysis showed that PamfT is developmentally regulated in the wild type and completely abolished in an amfR mutant. The −35 region of PamfT contained the consensus sequence for the binding of BldD, a pleiotropic negative regulator for morphological and physiological development in Streptomyces coelicolor A3(2). The cloned bldD locus of S. griseus showed high sequence similarity to the S. coelicolor counterpart. Transcription of bldD occurred constitutively in both the wild type and an A-factor-deficient mutant of S. griseus, which suggests that the regulatory role of BldD is independent of A-factor. The gel retardation assay revealed that purified BldD and AmfR recombinant proteins specifically bind PamfT. Overproduction of BldD in the wild-type cell conferred a bald phenotype (defective in aerial growth and streptomycin production) and caused marked repression of PamfT activity. An amfT-depleted mutant also showed a bald phenotype but PamfT activity was not affected. Both the bldD-overproducing wild-type strain and the amfT mutant were unable to induce aerial growth of an amfS mutant in a cross-feeding assay, which indicates that these strains are defective in the production of an active AmfS peptide. The results overall suggests that two independent regulators, AmfR and BldD, control PamfT activity via direct binding to determine the transcriptional level of the amf operon responsible for the production and secretion of AmfS peptide, which induces the erection of aerial hyphae in S. griseus.
EPIZOOTIOLOGY OF MYXOBOLUS CEREBRALIS, THE CAUSATIVE AGENT OF SALMONID WHIRLING DISEASE IN THE ROCK CREEK DRAINAGE OF WEST-CENTRAL MONTANA

Whirling disease, caused by the myxozoan parasite Myxobolus cerebralis, remains a health threat to salmonid fish in the western United States. Although various aspects of this host–parasite system have been studied, investigations examining the overall epizootiology of whirling disease in an ecosystem are lacking. Therefore, in June 1998, studies were initiated in the Rock Creek watershed of west-central Montana and continued through 2003 to assess the intensity of infection in trout using sentinel cages stationed throughout the drainage. Additional studies determined the percentage of the annelid worm, Tubifex tubifex, releasing M. cerebralis at various localities in Rock Creek and whether there was a seasonal or daily periodicity in the release of the triactinomyxon stage of the parasite from T. tubifex. Lastly, habitat and water quality parameters, and the effects of habitat restoration on transmission of M. cerebralis, were assessed. Overall, the intensity of M. cerebralis infections in sentinel trout increased significantly throughout the drainage between June of 1998 and 2003, with the biggest jump occurring between 1998 and 1999. In addition, the range of M. cerebralis expanded considerably over the period of study. There was no strict correlation between habitat condition and the occurrence of the parasite; fish became heavily infected in optimal and marginal habitats. However, fish exposed at a locality that had the lowest habitat ranking consistently had the highest intensity of infection. The parasite has apparently caused a dramatic decline in rainbow trout densities, but the brown trout population numbers have increased, and the overall fish density remains high. Although a major habitat restoration project did not seem to have an effect on decreasing disease intensity, this was not surprising because the restored area was located just downstream from a “hotspot” of infected T. tubifex.
Light-induced vibrational structure in H2+ and D2+ in intense laser fields.

Molecular bond-softening and above-threshold dissociation of H[sub 2][sup +] and D[sub 2][sup +] in intense laser fields is reexamined using 160 fs pulses of 769 nm light. At intensities greater than [similar to]10[sup 13] W/cm[sup 2] new features appear in the dissociation spectrum. These are consistent with the formation of trapped population in light-induced vibrational states, formed in the adiabatic potential near the three-photon resonance between the 1[ital s][sigma][sub [ital g]] and 2[ital p][sigma][sub [ital u]] states. Rovibrational structure of such light-induced states appears in the kinetic energy spectra of the ion fragments detected after multiphoton ionization.
Caught in the Crossfire: Forest-Dependent Poor People in Nepal

This paper examines the impact of armed conflict on the lives of the forest-dependent poor in Nepal. Based on a survey study carried out in four districts among forest-dependent poor and their service providers, the findings show that the armed conflict is severely affecting the lives and living conditions of the poor. The lack of food, drinking water, education, health care and employment opportunities has made them more vulnerable. The conflict has contributed on the disruption of social security, communal bonds, friendship and brotherhoods, trust and local hospitalities and it has planted frustration in these populations. Optimism of the poor is waning. However, they still want to see peace restored.Priority Problems of Forest Dependent Poor People in conflict situation in Nepal Keywords : forest-dependent poor, poverty, insurgency, poor doi: 10.3126/jfl.v5i1. 1975 Journal of Forest and Livelihood 5(1) February, 2006 pp.14-21
Lysosomal Glycosphingolipid Recognition by NKT Cells

NKT cells represent a distinct lineage of T cells that coexpress a conserved αβ T cell receptor (TCR) and natural killer (NK) receptors. Although the TCR of NKT cells is characteristically autoreactive to CD1d, a lipid-presenting molecule, endogenous ligands for these cells have not been identified. We show that a lysosomal glycosphingolipid of previously unknown function, isoglobotrihexosylceramide (iGb3), is recognized both by mouse and human NKT cells. Impaired generation of lysosomal iGb3 in mice lacking β-hexosaminidase b results in severe NKT cell deficiency, suggesting that this lipid also mediates development of NKT cells in the mouse. We suggest that expression of iGb3 in peripheral tissues may be involved in controlling NKT cell responses to infections and malignancy and in autoimmunity.
Combining retinoic acid and oral arsenic may be potentially the first-line therapy for non-high-risk acute promyelocytic leukemia.

Once regarded as a rapidly fatal disease, acute promyelocytic leukemia (APL) is now curable in most cases with the use of targeted treatment alone and without chemotherapy (CHT) (1). Platzbecker et al . (2) reported a prospective, randomized, multicenter, open-label, phase III noninferiority trial, which demonstrated the advantages of all-trans-retinoic acid (ATRA) and intravenous ATO over ATRA and CHT with significantly greater and more sustainable antileukemic efficacy over time for non-high-risk APL. The recent paper by Iland et al . (3) also revealed that ATRA and arsenic in initial therapy induction and consolidation for APL reduced the risk of relapse compared with historical controls. These studies demonstrated the advantages of combining ATRA and intravenous ATO over ATRA and CHT for non-high-risk APL.
Parental representation in twins discordant for schizophrenia

Synopsis Parental representation was assessed with the Parental Bonding Instrument (PBI) in 12 monozygotic (MZ) and 19 dizygotic (DZ) same-sexed twin pairs discordant for DSM-III-R schizophrenia. The schizophrenic twins reported less care and more overprotection from both parents than the non-schizophrenic co-twins. Multiple regression analysis disclosed that the results were independent of sex and age. Furthermore, the analysis demonstrated that whether the twins were monozygotic or dizygotic had no impact on the results. A stepwise discriminant analysis showed that difference in perceived paternal protection was the most important variable distinguishing between schizophrenic probands and their non-schizophrenic co-twins.
Gastrointestinal Manifestations of Amyloidosis

We reviewed gastrointestinal manifestations in 40 patients with amyloidosis. Gastrointestinal symptoms included anorexia, macroglossia, intestinal pseudo-obstruction, and altered bowel habits. Hepatomegaly was detected in eight patients, but none had clinically significant infiltrative liver disease. Mucosal friability and erosions were common endoscopic findings. Barium enema was noncontributory in the diagnosis of amyloidosis, since colonoscopy disclosed mucosal abnormalities in three of six patients with normal radiographic findings. Rectal biopsy had the highest diagnostic yield, followed by duodenal, gastric, and colonic biopsies.
Monoclonal antibody AG7 inhibits fertilization post sperm‐zona binding

Monoclonal antibodies (mAbs) against sperm cells are currently being used in an effort to define spermatozoal antigens involved in the fertilization process. We have produced a number of anti‐human sperm mAbs by immunization of female mice with the 100,000 × g supernatant of octylglycoside‐solubilized washed human sperm. From a panel of mAbs, 1 antibody, AG7, was selected and characterized due to its fertilization‐inhibiting characteristics. MAb AG7 defines a sperm acrosome antigen‐1 (SAA‐1) located in the acrosomal region of human sperm as evaluated by indirect immunofluorescence. Staining of life sperm cells indicated that the antigen is present on the sperm surface. SAA‐1 was also found on sperm of several other mammalian species, implying evolutionary conservation of the antigen. SAA‐1 was first observed on testicular sperm and can be followed through epididymal transit, ejaculation, and capacitation. When applied in a mouse in vitro fertilization assay, mAb AG7 inhibits fertilization by greater than 95%, and inhibition is dose dependent, with half‐maximal inhibition at 0.8 μg/ml. The block to fertilization could not be attributed to sperm agglutination, inhibition of motility, interference with adhesion to the zona pellucida, or inhibition of fusion with the oocyte membrane. MAb AG7 was demonstrated to inhibit calcium influx in spermatozoa in vitro (measured using the fluorescent indicator fura 2), a prerequisite for the acrosome reaction. Initial biochemical characterization of the antigen suggests it is proteinlike in nature, with a molecular weight of approximately 220 kD. The results suggest that SAA‐1, identified by mAb AG7, is a sperm antigen crucially involved in the fertilization process, possibly an atypical steriod receptor or ion channel located within the sperm plasma membrane. © 1992 Wiley‐Liss, Inc.
Fluoxetine for the treatment of childhood anxiety disorders.

OBJECTIVE To assess the efficacy and tolerability of fluoxetine for the acute treatment of children and adolescents with generalized anxiety disorder, separation anxiety disorder, and/or social phobia. METHOD Anxious youths (7-17 years old) who had significant functional impairment were randomized to fluoxetine (20 mg/day) (n = 37) or placebo (n = 37) for 12 weeks. RESULTS Fluoxetine was effective in reducing the anxiety symptoms and improving functioning in all measures. Using intent-to-treat analysis, 61% of patients taking fluoxetine and 35% taking placebo showed much to very much improvement. Despite this improvement, a substantial group of patients remained symptomatic. Fluoxetine was well tolerated except for mild and transient headaches and gastrointestinal side effects. Youths with social phobia and generalized anxiety disorder responded better to fluoxetine than placebo, but only social phobia moderated the clinical and functional response. Severity of the anxiety at intake and positive family history for anxiety predicted poorer functioning at the end of the study. CONCLUSIONS Fluoxetine is useful and well tolerated for the acute treatment of anxious youths. Investigations regarding the optimization of treatment to obtain full anxiety remission and the length of treatment necessary to prevent recurrences are warranted.
Detrimental effects of particulate matter on the pulmonary circulation.

To the Editor. — The communication by Shapiro et al1concerning fatal drug reactions among medical inpatients reports four deaths that resulted from fluid overload (pulmonary edema). We would like to point out another possible cause-effect relationship that may be responsible for the pulmonary edema. A two-year ongoing study of commercially available infusion fluids at Temple University Hospital2,3has revealed infusion fluids to contain a significant amount of foreign material (particulate matter). Analysis of over 1,000 commercially available solutions has revealed a content of foreign particles (glass, rubber, plastic, etc) of size above 5μ on the order of 100 particles/liter for one supplier. Two other suppliers had average particle counts of approximately 350 particles/liter. Over 1,-500 particles/liter were discovered in solutions of a fourth manufacturer. Although the clinical significance and the biological effects of these particles is unclear, some reports speculating on their clinical significance have appeared in the
Clinical Outcome of a Randomized Controlled Blinded Trial of Open Versus Laparoscopic Nissen Fundoplication in Infants and Children

Objective: To compare the clinical outcome and endocrine response in children who were randomized to open or laparoscopic Nissen fundoplication using minimization. Background: It is assumed that laparoscopic surgery is associated with less pain, quicker recovery and dampened endocrine response. Few randomized studies have been performed in children. Methods: Parents gave informed consent, and this study was approved and registered (ClinicalTrials.gov Identifier: NCT00231543). Anesthesia, postoperative analgesia and feeding were standardized. Parents and staff were blinded to allocation. Blood was taken for markers of endocrine response. Results: Twenty open and 19 laparoscopic patients were comparable with respect to age, weight, neurological status, and presence of congenital anomalies. Median time to full feeds was 2 days in both groups (P = 0.85); hospital stay was 4.5 days in the open group versus 5.0 days in the laparoscopic group (P = 0.57). Pain was adequately managed in both groups and there was no difference in morphine requirements. Median follow-up was 22 (range 12–34) months. Dysphagia, recurrence and need for redo fundoplication were not different between groups; retching was higher after open surgery (56% vs. 6%; P = 0.003). Insulin levels decreased at 24 hours, and was 54% lower (P = 0.02) after laparoscopy. Cortisol was elevated immediately postoperative, but was 42% lower (P = 0.02) after laparoscopy. Conclusions: There was no difference in the postoperative analgesia requirements and recovery. Laparoscopy decreased insulin levels to a greater extent, but caused less of a response in cortisol. Early postoperative outcome confirmed equal efficacy, but fewer children with retching after laparoscopy.
CMMI ( SW , DEV , SVC ) Compliance of SDLCs : a Service System View

In this paper a high-level strategic conceptual assessment on the extent of compliance of the three main Software Development Lifecycles (SDLCs) STD, RUP, and MSF-CMMI, with three of the main CMMI schemes (SW, DEV, and SVC) is reported. While that the SDLCs theme is a permanent and shared topic in information systems and software engineering research, however, the compliance of SDLCs with IT standards has been few explored. Our research goal is to establish an initial high-level strategic assessment on how the most usual SDLCs satisfy three of the main CMMI schemes. Compliance analysis is based on: (i) previous results reported in literature, (ii) a comparison of the CMMI specific goals of each process area versus the generic SDLCs core workflows descriptions, and (iii) joint academic and research expertise in SW standards from authors. This paper contributes an initial assessment which should be considered from a strategic view due to the coarse unit of analysis. A finer grain analysis in the level of SLDCs’ workflows and activities versus CMMI’s specific practices and typical work products is suggested.
Robust UV/VUV/EUV PureB Photodiode Detector Technology With High CMOS Compatibility

This paper gives an assessment of old and new data relevant to the optical and electrical performance of PureB photodiodes for application in the wavelength range 2 nm to 400 nm. The PureB layer, fabricated by depositing pure boron on Si, forms the anode region of devices that function as p+n junction diodes. The results show that the high sensitivity and high stability of the PureB diodes is related to the integrity of the interface with the Si. When measures are taken to retain a complete PureB coverage, thermal processing steps with minute long exposure to temperatures up to 900 °C do not compromise the robustness and a lower-than-ideal but still high responsivity is maintained. Besides the thermal processing considerations, other aspects that impact the integration of PureB in CMOS are reviewed.