Miracle-dz/UniFAR-FTUs huggingface dataset:
Conformation of a Group 2 Late Embryogenesis Abundant Protein from Soybean. Evidence of Poly (l-Proline)-type II Structure1

Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (l-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (l-proline)-type II-like helical conformation at 12°C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80°C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt α-helical structure and to interact with phospholipid bilayers through amphipathic α-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic stress-related damage to macromolecular structures.
Multiple Resources and Mental Workload

Objective: The objective is to lay out the rationale for multiple resource theory and the particular 4-D multiple resource model, as well as to show how the model is useful both as a design tool and as a means of predicting multitask workload overload. Background: I describe the discoveries and developments regarding multiple resource theory that have emerged over the past 50 years that contribute to performance and workload prediction. Method: The article presents a history of the multiple resource concept, a computational version of the multiple resource model applied to multitask driving simulation data, and the relation of multiple resources to workload. Results: Research revealed the importance of the four dimensions in accounting for task interference and the association of resources with brain structure. Multiple resource models yielded high correlations between model predictions and data. Lower correlations also identified the existence of additional resources. Conclusion: The model was shown to be partially relevant to the concept of mental workload, with greatest relevance to performance breakdowns related to dual-task overload. Future challenges are identified. Application: The most important application of the multiple resource model is to recommend design changes when conditions of multitask resource overload exist.
Can News About the Future Drive the Business Cycle?

We propose a model that generates an economic expansion in response to good news about future total factor productivity (TFP) or investment-specific technical change. The model has three key elements: variable capital utilization, adjustment costs to investment, and preferences that exhibit a weak short-run wealth effect on the labour supply. These preferences nest the two classes of utility functions most widely used in the business cycle literature as special cases. Our model can generate recessions that resemble those of the post-war U.S. economy without relying on negative productivity shocks. The recessions are caused not by contemporaneous negative shocks but rather by lackluster news about future TFP or investment-specific technical change.
OUTCOMES AFTER REPEAT TRANSSPHENOIDAL SURGERY FOR RECURRENT CUSHING'S DISEASE

OBJECTIVETo systematically analyze patient outcomes after repeat transsphenoidal (TS) surgery for recurrent Cushing's disease. METHODSWe retrospectively reviewed records of all patients with recurrent Cushing's disease who underwent repeat TS surgery for resection of a pituitary corticotroph adenoma at the University of Virginia Medical Center from 1992 to 2006. Remission at follow-up was defined as a normal postoperative 24-hour urine free cortisol, or continued need for glucocorticoid replacement after repeat TS surgery. Recurrence of the disease was defined as an elevated 24-hour urine free cortisol with clinical symptoms consistent with Cushing's disease while not receiving glucocorticoid replacement. Multivariate logistic regression was performed to evaluate the effect of potential predictors on remission. Recurrence rates, subsequent treatments, and the final endocrine status of the patients are presented. RESULTSWe identified 36 patients who underwent repeat TS surgery for recurrent Cushing's disease. The mean age of the patients was 40.3 years (range, 17.1–63.0 yr), and 26 were women. The median time to recurrence after initial successful TS surgery was 36 months (range, 4 mo–16 yr). Remission after repeat TS surgery was observed in 22 (61%) of the 36 patients. During the same time period, of the 338 patients who underwent first-time TS surgery for Cushing's disease, remission was achieved in 289 (85.5%). The odds of failure (to achieve remission) for patients with repeat TS surgery for recurrent Cushing's disease were 3.7 times that of patients undergoing first-time TS surgery (odds ratio, 3.7; 95% confidence interval, 1.8–7.8). Two of the 22 patients with successful repeat TS surgery had a second recurrence at 6 and 11 months, respectively. Complete biochemical and clinical remission after stereotactic radiosurgery, adrenalectomy, and ongoing ketoconazole therapy was achieved in 30 (83.3%) of the 36 patients, and active disease continued in 6 patients (16.7%). CONCLUSIONAlthough the success of repeat TS surgery for recurrence of Cushing's disease is less than that of initial surgery, a second procedure offers a reasonable possibility of immediate remission. If the operation is not successful, other treatments, including pituitary radiation, medical therapy, and even bilateral adrenalectomy, are required.
Consumers in Context: The BPM Research Program

This book presents a collection of papers by Gordon Foxall charting the development of the behavioural perspective model (BPM) which he devised in the early 1980s and subsequently developed. The model offers a unique behaviour-based theory of consumer choice in relation to circumstances by locating consumer behaviour in the interaction of individual and situation. Presenting a unique view of how consumer behaviour works, what motivates it and what its functions are, Gordon Foxall goes on to apply this knowledge to our understanding of how marketing management itself works, offering an equally novel perspective on what marketing is and what it does. Bringing alive the subject of economic consumption, this seminal volume should be of interest to students and researchers in consumer research.
Serum hepcidin-25 levels predict the progression of renal anemia in patients with non-dialysis chronic kidney disease.

BACKGROUND Hepcidin is associated with iron-restricted erythropoiesis. A previous cross-sectional study showed that serum hepcidin-25 levels are negatively associated with the hemoglobin concentration in non-dialysis chronic kidney disease (CKD) patients with sufficient iron stores. This longitudinal study aimed at ascertaining the association between hepcidin-25 levels and the progression of renal anemia. METHODS We selected 335 non-dialysis CKD patients who showed hemoglobin concentrations >10 g/dL and who were not receiving erythropoiesis-stimulating agent (ESA) therapy, from among the subjects of our previous study, who had been recruited between February and June 2007 in a previous study. The primary outcome was the start of the ESA therapy or hemoglobin concentrations remaining below 10 g/dL for >3 months, by 31 December 2010. The patients were classified into high- and low-ferritin groups depending on their median ferritin levels. The Cox proportional hazard model with restricted cubic spline curve analysis was used to determine the association between hepcidin-25 levels and the outcome for each group. RESULTS The hepcidin-25 level was a significant predictor both for the high-ferritin group (P = 0.04, linearity = 0.02) and for the low-ferritin group (P = 0.04, linearity P = 0.02). The spline curve for the high-ferritin group showed that higher hepcidin-25 levels had a high log-relative hazard. CONCLUSIONS Higher hepcidin-25 levels predict the progression of anemia in non-dialysis CKD patients with sufficient iron stores, indicating the involvement of hepcidin in the progression of anemia in non-dialysis CKD patients.
Inherited Determinants of Ovarian Cancer Survival

Purpose: Due to variation of outcome among cases, we sought to examine whether overall survival in ovarian cancer was associated with common inherited variants in 227 candidate genes from ovarian cancer–related pathways including angiogenesis, inflammation, detoxification, glycosylation, one-carbon transfer, apoptosis, cell cycle regulation, and cellular senescence. Experimental Design: Blood samples were obtained from 325 women with invasive epithelial ovarian cancer diagnosed at the Mayo Clinic from 1999 to 2006. During a median follow-up of 3.8 years (range, 0.1-8.6 years), 157 deaths were observed. Germline DNA was analyzed at 1,416 single nucleotide polymorphisms (SNP). For all patients, and for 203 with serous subtype, we assessed the overall significance of each gene and pathway, and estimated risk of death via hazard ratios (HR) and 95% confidence intervals (CI), adjusting for known prognostic factors. Results: Variation within angiogenesis was most strongly associated with survival time overall (P = 0.03) and among patients with serous cancer (P = 0.05), particularly for EIF2B5 rs4912474 (all patients HR, 0.69; 95% CI, 0.54-0.89; P = 0.004), VEGFC rs17697305 (serous subtype HR, 2.29; 95% CI, 1.34-3.92; P = 0.003), and four SNPs in VHL. Variation within the inflammation pathway was borderline significant (all patients, P = 0.09), and SNPs in CCR3, IL1B, IL18, CCL2, and ALOX5 which correlated with survival time are worthy of follow-up. Conclusion: An extensive multiple-pathway assessment found evidence that inherited differences may play a role in outcome of ovarian cancer patients, particularly in genes within the angiogenesis and inflammation pathways. Our work supports efforts to target such mediators for therapeutic gain. Clin Cancer Res; 16(3); 995–1007
Ocular Risk Factors for Exudative AMD: A Novel Semiautomated Grading System

Purpose. To evaluate the contribution of the ocular risk factors in the conversion of the fellow eye of patients with unilateral exudative AMD, using a novel semiautomated grading system. Materials and Methods. Single-center, retrospective study including 89 consecutive patients with unilateral exudative AMD and ≥3 years of followup. Baseline color fundus photographs were graded using an innovative grading software, RetmarkerAMD (Critical Health SA). Results. The follow-up period was 60.9 ± 31.3 months. The occurrence of CNV was confirmed in 42 eyes (47.2%). The cumulative incidence of CNV was 23.6% at 2 years, 33.7% at 3 years, 39.3% at 5 years, and 47.2% at 10 years, with a mean annual incidence of 12.0% (95% CI = 0.088–0.162). The absolute number of drusen in the central 1000 and 3000 μm (P < 0.05) and the absolute number of drusen ≥125 µm in the central 3000 and 6000 µm (P < 0.05) proved to be significant risk factors for CNV. Conclusion. The use of quantitative variables in the determination of the OR of developing CNV allowed the establishment of significant risk factors for neovascularization. The long follow-up period and the innovative methodology reinforce the value of our results. This trial is registered with ClinicalTrials.gov NCT00801541.
In vitro positive selection and anergy induction of class II-restricted TCR transgenic thymocytes by a cortical thymic epithelial cell line.

Thymic epithelial cell lines isolated from hyperplastic thymi of transgenic mice over-expressing human papilloma viral oncogenes E6 and E7 constitutively displayed a phenotype consistent with a cortical origin. Exposure to IFN-gamma induced class II MHC and ICAM-1 expression, and up-regulated expression of VCAM-1 and class I MHC molecules. CD40 expression was maximally induced by a combination of IFN-gamma and IL-1, with lower levels of induction observed with a mixture of IFN-gamma and tumor necrosis factor (TNF)-alpha or TNF-alpha alone. B7-1 or B7-2 was not expressed constitutively or in response to cytokines. These stromal cells supported the development of CD4 single-positive (SP) cells in reaggregate co-cultures with CD4+ CD8+ thymocytes from TCR transgenic mice, but did not stimulate class II MHC-restricted, moth cytochrome c (MCC)-reactive T cells in vitro. The behavior of the culture system was consistent with positive selection, i.e. increased numbers of CD4 SP cells, gain of antigen responsiveness, and requirement for epithelial class II MHC products. Some variants of these stromal cell lines required exogenous MCC peptide in the reaggregation cultures (RC) for positive selection to occur. While a low concentration of MCC peptide (0.01-0.1 microM) significantly enhanced the accumulation of CD4 SP cells, higher concentrations of peptide (1-10 microM) resulted in recovery of predominantly CD4- CD8- and CD4(low) CD8- cells. Thymocytes recovered from RC containing low, but not high concentrations of peptide responded to MCC peptide in secondary cultures with splenic antigen-presenting cells.
Secular trends for age at spermarche among Chinese boys from 11 ethnic minorities, 1995–2010: a multiple cross-sectional study

Objectives We compared the differences in median age at spermarche among 11 ethnic minorities in 2010, estimated the trends regarding age at spermarche in different ethnic minorities from 1995 to 2010, and explored the association of spermarche with body mass index (BMI). Methods We used four cross-sectional Chinese National Surveys on Students’ Constitution and Health (CNSSCH, 1995, 2000, 2005 and 2010), and the total sample size was 40 113 children aged 11–18 years. The median age at spermarche of each ethnic minority was determined by using probit analysis. Logistic regression was used to assess the association of spermarche with BMI. Results In 2010, the ethnic minorities with earliest age at spermarche were Qiang (12.03 years), Zhuang (12.91 years) and Kirghiz (13.17 years); the three ethnic minorities with latest age at spermarche were Dong (14.73 years), Yao (14.60 years), and Naxi (14.36 years). From 1995 to 2010, age at spermarche showed a decline in almost each minority group except Yao and Dong. A higher BMI was associated with an increased likelihood of having reached spermarche after adjusting for age, regions or ethnic minorities. Conclusions A large variation in age at spermarche was observed among different ethnic minorities. The age at spermarche showed a downward shift in almost each of the 11 ethnic minorities with different patterns over time, and the children with higher BMI are more likely to enter puberty early.
Two-loop splitting functions in QCD

We present the universal two-loop splitting functions that describe the limits of two-loop n-point amplitudes of massless particles when two of the momenta are collinear. To derive the splitting amplitudes, we take the collinear limits of explicit two-loop four-point helicity amplitudes computed in the 't Hooft-Veltman scheme. The g ? gg splitting amplitude has recently been computed using the unitarity sewing method and we find complete agreement with the results of ref. [1]. The two-loop q ? qg and g ? q splitting functions are new results. We also provide an expression for the two-loop soft splitting function.
Crystal Structure of the Dengue Virus RNA-Dependent RNA Polymerase Catalytic Domain at 1.85-Angstrom Resolution

ABSTRACT Dengue fever, a neglected emerging disease for which no vaccine or antiviral agents exist at present, is caused by dengue virus, a member of the Flavivirus genus, which includes several important human pathogens, such as yellow fever and West Nile viruses. The NS5 protein from dengue virus is bifunctional and contains 900 amino acids. The S-adenosyl methionine transferase activity resides within its N-terminal domain, and residues 270 to 900 form the RNA-dependent RNA polymerase (RdRp) catalytic domain. Viral replication begins with the synthesis of minus-strand RNA from the dengue virus positive-strand RNA genome, which is subsequently used as a template for synthesizing additional plus-strand RNA genomes. This essential function for the production of new viral particles is catalyzed by the NS5 RdRp. Here we present a high-throughput in vitro assay partly recapitulating this activity and the crystallographic structure of an enzymatically active fragment of the dengue virus RdRp refined at 1.85-Å resolution. The NS5 nuclear localization sequences, previously thought to fold into a separate domain, form an integral part of the polymerase subdomains. The structure also reveals the presence of two zinc ion binding motifs. In the absence of a template strand, a chain-terminating nucleoside analogue binds to the priming loop site. These results should inform and accelerate the structure-based design of antiviral compounds against dengue virus.
The P gene product of hepatitis B virus is required as a structural component for genomic RNA encapsidation

Encapsidation of the pregenomic RNA into nucleocapsids is a selective process which depends on specific RNA-protein interactions. The signal involved in the packaging of the hepatitis B virus (HBV) RNA pregenome was recently defined as a short sequence located near the 5' end of that molecule (Junker-Niepmann et al., EMBO J., in press), but it remained an open question which viral proteins are required. Using a genetic approach, we analyzed whether proteins derived from the HBV P gene play an important role in pregenome encapsidation. The results obtained with point mutations, deletions, and insertions scattered throughout the P gene clearly demonstrate that (i) a P gene product containing all functional domains is required both for the encapsidation of HBV pregenomic RNA and for packaging of nonviral RNAs fused to the HBV encapsidation signal, (ii) known enzymatic activities are not involved in the packaging reaction, suggesting that P protein is required as a structural component, and (iii) P protein acts primarily in cis, i.e., pregenomic RNAs from which P protein is synthesized are preferentially encapsidated.
Extracting Clauses for Spoken Language Understanding in Conversational Systems

Spontaneous human utterances in the context of human-human and human-machine dialogs are rampant with dysfluencies, and speech repairs. Furthermore, when recognized using a speech recognizer, these utterances produce a sequence of words with no identification of clausal units. Such long strings of words combined with speech errors pose a difficult problem for spoken language parsing and understanding. In this paper, we address the issue of editing speech repairs as well as segmenting user utterances into clause units with a view of parsing and understanding spoken language utterances. We present generative and discriminative models for this task and present evaluation results on the human-human conversations obtained from the Switch board corpus.
Acute skin toxicity in Korean breast cancer patients carrying BRCA mutations

Abstract Purpose: In contrast to in vitro studies, most clinical trials testing the radiosensitivity of BRCA (Breast cancer susceptibility gene) mutations do not find a correlation between BRCA status and enhanced radiosensitivity. These trials include different ethnicities, and there is a lack of clinical data on BRCA1/2 mutation carriers and radiosensitivity in non-Caucasian patients. The goal of this study was to investigate acute skin toxicity, as a part of radiosensitivity, in breast cancer patients with BRCA1/2 mutations. Material and methods: BRCA mutation analysis was performed for 213 patients who underwent breast-conserving therapy using radiotherapy. Skin toxicity was scored according to the Radiation Therapy Oncology Group (RTOG) criteria during treatment and during one-month follow-up after radiation therapy. Results: Forty-six patients had BRCA1/2 mutations and 57 patients showed higher than grade 2 (RTOG) skin toxicity. In multivariate analysis, significant associations were found between mean breast volume and acute skin toxicity. BRCA mutation status, however, failed to show a significant correlation. Conclusions: Our results indicate that carriers of BRCA1/2 mutations among non-Caucasian breast cancer patients showed no enhancement in radiation sensitivity. Multiple genetic markers may be correlated with normal tissue responses after radiotherapy. Further studies are needed to identify genetic predispositions to normal tissue responses after radiotherapy.
TaggerOne: joint named entity recognition and normalization with semi-Markov Models

MOTIVATION Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization. METHODS We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput. RESULTS We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance. AVAILABILITY AND IMPLEMENTATION The TaggerOne source code and an online demonstration are available at: http://www.ncbi. nlm.nih.gov/bionlp/taggerone CONTACT zhiyong.lu@nih.gov SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.