Miracle-dz/UniFAR-FTUs huggingface dataset:
Diverse Gene Junctions of Respiratory Syncytial Virus Modulate the Efficiency of Transcription Termination and Respond Differently to M2-Mediated Antitermination

ABSTRACT The ability of the diverse gene junctions of respiratory syncytial (RS) virus to signal the termination of transcription was analyzed. Nine dicistronic subgenomic replicons of RS virus were constructed; each contained one of the RS virus gene junctions in its natural upstream and downstream sequence context. The RNA synthesis activities of these subgenomic replicons were analyzed in the absence and presence of the M2 protein, which we showed previously to function as a transcription antiterminator. Our data showed that the efficiency with which the polymerase terminated transcription was affected by the gene junction that it encountered. The M2 protein significantly decreased the efficiency of the termination of transcription, resulting in increased levels of readthrough transcription at all the gene junctions. The diverse gene junctions fell into three broad groups with respect to their ability to signal transcription termination. One group of gene junctions (NS1/NS2, NS2/N, M2/L, and L/trailer) showed inefficient termination in the absence or the presence of the M2 protein. A second group of gene junctions (N/P, P/M, M/SH, SH/G, and G/F) terminated transcription efficiently. The SH/G gene junction terminated transcription with the greatest efficiency and produced low levels of readthrough transcripts in the absence or the presence of the M2 protein, correlating with the absence of SH/G polycistronic transcripts in RS virus-infected cells. The F/M2 gene junction was particularly sensitive to the M2 protein: it efficiently signaled termination in the absence of the M2 protein but produced high levels of readthrough transcripts in the presence of the M2 protein. This result suggests that the M2 protein may regulate its own production by negative feedback. The data presented here show that the different gene junctions of RS virus do modulate RS virus transcription termination. The M2 protein reduced termination at all gene junctions. The magnitude of antitermination due to the M2 protein, however, varied at the different gene junctions. The data presented here indicate that the mechanism for the regulation of RS virus gene expression is more complex than was previously appreciated.
Numberical taxonomic analysis of some slowly growing mycobacteria using hypothetical median strain patterns.

SUMMARY: The reactions of 1498 isolates of slowly growing mycobacteria in 50 character states have been compared to those of 17 hypothetical median strain patterns. The establishment of intra- and intertaxon matching values for clusters so generated, allowed certain aggregates of taxa to be recognized for which a conventional n × n matching matrix might provide more clear cut taxonomic definition of species. Those species which are clearly distinct from the others include Mycobacterium tuberculosis, M. bovis, M. kansasii, M. flavescens, M. xenopi and M. gastri. Problems still exist regarding the precise separation of taxa within Runyon Groups II (M. scrofulaceum, M. gordonae and IIIB) and Group III (M. avium—M. intracellulare and M. terrae—M. nonchromogenicum—M. novum—M. triviale). These latter are discussed.
Dendritic Cells Loaded With Killed Allogeneic Melanoma Cells can Induce Objective Clinical Responses and MART-1 Specific CD8+ T-cell Immunity

Dendritic cells (DCs) loaded with killed allogeneic tumors can cross-prime tumor-specific naive CD8+ T cells in vitro, thereby providing an option to overcome human leukocyte antigen restriction inherent to loading DC vaccines with peptides. We have vaccinated 20 patients with stage IV melanoma with autologous monocyte-derived DCs loaded with killed allogeneic Colo829 melanoma cell line. DCs were generated by culturing monocytes with granulocyte macrophage-colony stimulating factor (granulocyte macrophage-colony stimulating factor) and interleukin (IL-4) and activated by additional culture with tumor necrosis factor and CD40 ligand. A total of 8 vaccines were administered at monthly intervals. The first patient was accrued December 2002 and the last November 2003. Fourteen patients were alive at 12 months, 9 patients were alive at 24 months, and 8 patients are alive as of January 2006. The estimated median overall survival is 22.5 months with a range of 2 to 35.5 months. Vaccinations were safe and tolerable. They induced, in 2 patients who failed previous therapy, durable objective clinical responses, 1 complete regression (CR) and 1 partial regression (PR) lasting 18 and 23 months, respectively. Three out of 13 analyzed patients showed T-cell immunity to melanoma antigen recognized by autologous T cells (MART-1) tissue differentiation antigen. Two of 3 patients showed improved immune function after vaccinations demonstrated by improved secretion of interferon (IFN)-γ or T-cell proliferation in response to MART-1 derived peptides. In one of these patients, vaccination led to elicitation of CD8+ T-cell immunity specific to a novel peptide-derived from MART-1 antigen, suggesting that cross-priming/presentation of melanoma antigens by DC vaccine had occurred. Thus, the present results justify the design of larger follow-up studies to assess the clinical response to DC vaccines loaded with killed allogeneic tumor cells in patients with metastatic melanoma.
Investigation of High Voltage Breakdown and Arc Localization in RF Structures

An effort is underway to improve the voltage standoff capabilities of ion cyclotron range of frequencies (ICRF) heating and current drive systems. One approach is to develop techniques for determining the location of an electrical breakdown (arc) when it occurs. A technique is described which uses a measurement of the reflection coefficient of a swept frequency signal to determine the arc location. The technique has several advantages including a requirement for only a small number of sensors and very simple data interpretation. In addition a test stand is described which will be used for studies of rf arc behavior. The device uses a quarter-wave resonator to produce voltages to 90 kV in the frequency range of 55-80 MHz.
Clinical Case Conference Prader-Willi Syndrome

Prader-Willi syndrome is a genetic disorder characterized by mental retardation, dysmorphic features, and behavioral dysfunction, most notably food-related problems such as hyperphagia, food seeking, and a high risk for obesity (1). Although food-related symptoms are a hallmark of the disorder, other psychiatric manifestations are common and can lead to significant interference in the affected individual’s development and functioning. Characteristic symptoms may include temper tantrums, oppositional behavior and stubbornness, emotional lability, and obsessive ruminations or compulsive behaviors such as skin-picking (2). In light of its distinctive behavioral, psychiatric, and genetic findings, PraderWilli syndrome has emerged as a model for genetic and neurodevelopmental disorders. A girl with PraderWilli syndrome illustrates the characteristics of the syndrome and its clinical management and suggests how Prader-Willi syndrome can serve as a heuristic model for other neuropsychiatric conditions.
Assessing the Critical Parameters of eSMART-MH: A Promising Avatar-Based Digital Therapeutic Intervention to Reduce Depressive Symptoms.

PURPOSE To assess, from the young adults' (YAs') perspectives, the critical parameters (necessity, acceptability, feasibility, fidelity, and safety) of an avatar-based intervention, eSMART-MH, to reduce depressive symptoms. DESIGN AND METHODS YAs (n = 60) were randomly assigned to eSMART-MH or control and observed for 12 weeks. Qualitative and quantitative data were collected. FINDINGS Necessity, acceptability, fidelity, and safety of eSMART-MH were supported. Feasibility results were mixed. When benchmarked against usual care, eSMART-MH demonstrated greater feasibility. PRACTICE IMPLICATIONS eSMART-MH is a promising digital therapeutic for depressive symptoms. Feasibility can be strengthened through "on the go" access via mobile devices and Internet delivery.
Measurement of pitch by subharmonic summation.

In order to account for the phenomenon of virtual pitch, various theories assume implicitly or explicitly that each spectral component introduces a series of subharmonics. The spectral-compression method for pitch determination can be viewed as a direct implementation of this principle. The widespread application of this principle in pitch determination is, however, impeded by numerical problems with respect to accuracy and computational efficiency. A modified algorithm is described that solves these problems. Its performance is tested for normal speech and "telephone" speech, i.e., speech high-pass filtered at 300 Hz. The algorithm out-performs the harmonic-sieve method for pitch determination, while its computational requirements are about the same. The algorithm is described in terms of nonlinear system theory, i.c. , subharmonic summation. It is argued that the favorable performance of the subharmonic-summation algorithm stems from its corresponding more closely with current pitch-perception theories than does the harmonic sieve.
Correlations of ALDH1 expression with molecular subtypes and ABCG2 in breast cancer.

OBJECTIVE To investigate the correlations of aldehyde dehydrogenase 1 (ALDH1) expression with the molecular subtypes and ATP-binding cassette subfamily G member 2 (ABCG2) in breast cancer. METHODS The specimens from 179 cases of breast cancer were divided into five molecular subtypes according to the immunological markers (ER, PR, HER2 and CK5/6), which were luminal A, luminal B, Her2-enriched, basal-like and breast-like subtype, respectively. The expressions of ALDH1 and ABCG2 of the specimens were detected with immunohistochemical staining, and the relationship between them as well as their relations with the clinicopathological factors of breast cancer was analyzed. RESULTS Of the 179 cases of breast cancer, ALDH1 positive expression was present in 43 cases (24.0%). The AIDH1 expression rate showed significant difference among the different molecular subtypes of breast cancer (P=0.003). The positive expression rate of ALDH1 was 16.7% (17/102) in luminal A subtype, 21.4% (3/14) in luminal B subtype, 54.5% (13/22) in Her2-enriched subtype, 33.3% (8/24) in basal-like subtype, and 17.6% (3/17) in breast-like subtype, respectively. The positive expression of ALDH1 had no significant relation with the ABCG2 expression (P=0.052). Both ALDH1 and ABCG2 expressions were related to the administration of preoperative chemotherapy (P=0.027 and P=0.033) and ALDH1 expression was related to the HER2 expression (P=0.006). CONCLUSIONS With a high expression level of ALDH1, HER2 overexpression, basal-like and ABCG2-positive types were associated with poor outcomes and treatment resistance in breast cancer. The expression of ALDH1 has no obvious relation with ABCG2.
A systematic review of honey uses and its potential value within oncology care.

AIM To synthesise the evidence regarding honey's role in health care and to identify whether this evidence applies more specifically to cancer care. DESIGN Systematic review. METHODS The inclusion and exclusion criteria were agreed by two reviewers and a keyword strategy was developed. EMBASE, CINAHL, AMED, MEDLINE, COCHRANE and PUBMED databases were screened to identify suitable articles. The citation list from each included study was also screened for potentially suitable papers. The key findings from each study were entered onto a data extraction sheet. RESULTS In total, 43 studies were included in the systematic review, which included studies in relation to wounds (n = 19), burns (n = 11), skin (n = 3), cancer (n = 5) and others (n = 5). In addition, a systematic review regarding honey use in wound care was also included. While the majority of studies noted the efficacy of honey in clinical use, five studies found honey to be equally as effective as the comparator and three found honey to be less effective than the comparator treatment. Other research did not illustrate any significant difference between standard treatment regimes vs. honey treatment. Studies were generally poor in quality because of small sample sizes, lack of randomisation and absence of blinding. CONCLUSIONS Honey was found to be a suitable alternative for wound healing, burns and various skin conditions and to potentially have a role within cancer care. RELEVANCE TO CLINICAL PRACTICE In the cancer setting, honey may be used for radiation-induced mucositis, radiotherapy-induced skin reactions, hand and foot skin reactions in chemotherapy patients and for oral cavity and external surgical wounds.
CARBON UPTAKE IN A MARINE DIATOM DURING ACUTE EXPOSURE TO ULTRAVIOLET B RADIATION: RELATIVE IMPORTANCE OF DAMAGE AND REPAIR 1

Experiments on a marine diatom, Thalassiosira pseudonana (Hustedt) clone 3H, demonstrate that under moderate photon flux densities (75 μmol quanta·m−2·s−1) of visible light the inhibition of photosynthesis by supplemental ultraviolet (UV) radiation (UV‐B: 280–320 nm) is well described as a hyperbolic function of UV‐B irradiance for time scales of 0.5–4 h. Results are consistent with predictions of a recently developed model of photosynthesis under the influence of UV and visible irradiance. Although net destruction of chlorophyll occurs during a 4‐h exposure to UV‐B, and the effect is a function of exposure, the principal effect of UV‐B is a decrease in chlorophyll‐specific photosynthetic rate. The dependence of photoinhibition on dosage rate, rather than cumulative dose, and the hyperbolic shape of the relationship are consistent with net photoinhibition being an equilibrium between damage and repair. The ratio of damage to repair is estimated by a mathematical analysis of the inhibition of photosynthesis during exposures to UV‐B. A nitrate‐limited culture was much more sensitive to UV‐B than were the nutrient‐replete cultures, but the kinetics of photoinhibition were similar. The analysis suggests that the nutrient‐limited culture was more sensitive than the nutrient‐replete cultures because repair or turnover of critical proteins associated with photosynthesis is inhibited. An inhibitor of chloroplast protein synthesis was used to suppress repair processes. Photoinhibition by UV‐B was enhanced, and inhibition was a function of cumulative dose, as would be expected if damage were not countered by repair. The fundamental importance of repair processes should be considered in the design of field experiments and models of UV‐B effects in the environment, especially in the context of vertical mixing. Repair processes must also be considered whenever biological weighting functions are developed.
Invasive Pulmonary Aspergillosis: Identification of Risk Factors

Aspergillosis is the second most frequent fungal infection after candidiasis in teaching hospitals. Clinical manifestations of pulmonary aspergillosis range from asymptomatic colonization to disseminated disease. The aim of this study was to identify the risk factors associated with invasive pulmonary aspergillosis, in patients with positive pulmonary isolation of Aspergillus species. A review was undertaken of all clinical records with pulmonary isolation of Aspergillus species at Reina Sofia University Hospital from January 1995 to December 1998. Data collected were: age, gender, history of smoking, past medical history, such as chronic pulmonary disease, immunosuppression, granulocytopenia in the past 6 months and during the last admission, history of surgery including within the last year of the study period, number of hospital admissions and clinical evidence of invasive pulmonary aspergillosis. To investigate all the possible risk factors for invasive pulmonary aspergillosis, a multivariable logistic regression model was used. 132 patients with positive pulmonary isolation were identified, of which 42.4% had clinical evidence of invasive pulmonary aspergillosis. The independent factors significantly associated with invasive pulmonary aspergillosis were: granulocytopenia in the past 6 months, immunosuppression in the last admission and the number of hospital admissions within the past year. Patients with a history of granulocytopenia in the past 6 months and immunosuppression in the last admission are the high-risk group for invasive pulmonary aspergillosis. However, invasive pulmonary aspergillosis can also occur in mild granulocytopenic or even immunocompetent patients.
A rule-based approach for automatic identification of publication types of medical papers

The medical domain has an abundance of textual resources of varying quality. The quality of medical articles depends largely on their publication types. However, identifying high-quality medical articles from search results is till date a manual and time-consuming process. We present a simple, rule-based, post-retrieval approach to automatically identify medical articles belonging to three high-quality publication types. Our approach simply uses title and abstract information of the articles to perform this. Our experiments show that such a rule-based approach has close to 100% precision and recall for the three publication types.
P-selectin gene haplotype associations with albuminuria in the Diabetes Heart Study.

BACKGROUND Adhesion molecules, such as P-selectin, play a pivotal role in leukocyte adhesion to the endothelium during inflammation. We investigated the relationship between P-selectin gene polymorphisms and albuminuria in 565 European American siblings (84% with type 2 diabetes) from 227 families participating in the Diabetes Heart Study (DHS). METHODS Three common missense P-selectin polymorphisms (S290N, N562D, and T715P) were genotyped. Albuminuria was defined as an albumin:creatinine ratio (ACR) > or = 17 mg/g in males, and > or = 25 mg/g in females. Tests of association were based on generalized estimating equations (GEE1) and tests of linkage disequilibrium were based on the quantitative pedigree disequilibrium test (QPDT). RESULTS Each copy of the 290Asn (S290N) allele was associated with a 45% absolute increase in ACR (P= 0.007), and a higher risk for the presence of albuminuria [odds ratio (OR), 1.71 for each 290A sn allele] (P= 0.002). Adjustment for other determinants of ACR, including stratification by age, gender, and presence of diabetes, did not alter these results. Haploytpe analyses using both GEE1 and QPDT methods revealed that the N-N-T haplotype, containing asparagine codons at sites S290N and N562D, was associated with an increased risk of albuminuria (OR 1.77) (P= 0.005, for each additional copy of the N-N-T haplotype). CONCLUSION The 290Asn (S290N) variant of P-selectin was associated with a higher prevalence and greater degree of albuminuria in European American siblings of type 2 diabetic families.
Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis

Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form protein self-assemblies, such as toxic or non-toxic aggregates and fibrils, and have been postulated to relate to diseases. These disease-related IDPs include Aβ(1-42) [Alzheimer's disease (AD)], Tau (AD and tauopathy), α-synuclein (Parkinson's disease) and p53 (cancer). Several studies suggest that these aggregation and/or fibril formation processes are often initiated by transient conformational changes of the IDPs prior to protein self-assembly. Interestingly, the pathological molecular processes of these IDPs share multiple common features with those of protein misfolding diseases, such as transmissible spongiform encephalopathy (PrPsc) and AL-amyloidosis (VL-domain of γ-immunoglobulin). This review provides an overview of solution NMR techniques that can help analyse the early and transient events of conformational equilibrium of IDPs and folded proteins.
Complementation of notabilis, an abscisic acid‐deficient mutant of tomato: importance of sequence context and utility of partial complementation

The abscisic acid (ABA)-deficient tomato mutant notabilis (not) is believed to be a null mutation in the gene LeNCED1 , encoding a 9- cis -epoxycarotenoid dioxygenase involved in ABA biosynthesis. We have sequenced and analysed a 19 kb genomic clone containing LeNCED1 and 5.4 kb of its promoter. This clone was transferred to not homozygotes and several non-wilty transformed plants were obtained. The basal ABA content, water relations, shoot and root growth, adventitious rooting, ethylene evolution and ability to accumulate ABA under water stress are described for two of these lines, not comp.13 and not comp.1 . Partial complementation was observed for most parameters measured for not comp.1 . Full complementation was observed in not comp.13 for all parameters measured in whole plants under well-watered and water-stressed conditions. These data provide further evidence that LeNCED1 is the wild-type allele of the not mutant gene. However, not comp.13 was unable to accumulate the wild-type levels of ABA in rapidly dehydrated leaves, indicating that it too was only partially complemented. Since LeNCED1 is an environmentally regulated gene encoding a rate-limiting enzyme, precise levels and patterns of gene expression may be needed to fully recreate wild-type phenotype. The utility of partially complemented lines to study the role of ABA in plant responses to stress conditions, and in promoter analysis, is discussed.
Using ontologies for reusing knowledge in the software development domain

As software systems become bigger and more complex, software developers need to cope with a growing amount of information and knowledge. The knowledge generated during the software development process can be a valuable asset for a software company. But in order to take advantage of this knowledge, the company must store and manage it for reuse. Ontologies are a powerful mechanism for representing knowledge and encoding its meaning. These structures can be used to model and represent the knowledge, stored in a knowledge management system and classify it according to the knowledge domain that the system supports. This paper describes the Semantic Reuse System (SRS), which takes advantage of ontologies, represented using the knowledge representation languages of the Semantic Web, for software development knowledge reuse. We describe how this knowledge is stored and the reasoning mechanisms that support the reuse.