Miracle-dz/UniFAR-FTUs huggingface dataset:
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of species and an important resource for annotation of genomic sequence. The TIGR Gene Indices (http://www.tigr.org/tdb/tgi. shtml) are a collection of species-specific databases that use a highly refined protocol to analyze EST sequences in an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed by first clustering, then assembling EST and annotated gene sequences from GenBank for the targeted species. This process produces a set of unique, high-fidelity virtual transcripts, or Tentative Consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, to provide links between orthologous and paralogous genes and as a resource for comparative sequence analysis.
Analysis of serum granulysin in patients with hematopoietic stem‐cell transplantation: Its usefulness as a marker of graft‐versus‐host reaction

Granulysin is a newly identified CTL/NK cell‐related cytotoxic protein, which is secreted in both constitutive and Ca‐dependent manner. To evaluate its significance in stem‐cell transplantation (SCT), serum granulysin was measured by newly established ELISA method in 26 patients undergoing SCT (21 allogeneic and 5 autologous). In the allogeneic SCT, granulysin was transiently increased in 3 weeks, which was not observed in autologous SCT. In acute GVHD, serum granulysin was markedly increased and correlated with the severity of GVHD. Elevation of granulysin was not necessarily associated with increase of sIL2R or IFN‐γ. In vitro, allospecific T cells released granulysin in an allo‐specific manner, and it was correlated with allo‐specific cytotoxic activity. These results indicate that increased release of granulysin presents alloreactivity and serum granulysin is useful as a marker of GVHD in SCT. Am. J. Hematol. 81:340–348, 2006. © 2006 Wiley‐Liss, Inc.
When Does Scene Categorization Inform Action Recognition?

When comprehending a film, viewers rapidly construct a working memory representation of the narrative called an event model. These models encode the story location first (Kitchen vs. Park) followed by the character's action (Cooking vs. Washing dishes)(Larson, Hendry, & Loschky, 2012). This time course for scene and action categorization was also supported by recent research showing that action recognition is best when it was embedded in real scenes than a gray background. Although, this benefit was not present at early processing times (< 50 ms SOA)(Larson, et al., 2013). This suggests that scene and action recognition are functionally isolated processes at early processing times. However, this conclusion may be an artifact of the design used. Namely, actions from the same scene category were presented in blocks, allowing participants in the gray background condition to predict the scene category that would be presented without relying on the scene's perceptual information. If true, then presenting actions in a random sequence should eliminate this advantage. Participants were assigned to one of three different viewing conditions. Actions were presented either in their original scene background, on a neutral gray background, or on a texture background generated from the original scene (Portilla & Simoncelli, 2000). Visual masking was used to control processing time which varied from 24 to 365 ms SOA. Afterwards, a valid or invalid action category post-cue was presented requiring participants to make a Yes/No response. The results show no difference between the original and gray background conditions at early processing times (< 50 ms SOA), but both conditions were better than the texture background. After 50 ms SOA, performance for the original background was greater than the gray and texture conditions. The data indicates that sufficient scene categorization processing (~ 50 ms SOA) is required before it can inform action categorization. Meeting abstract presented at VSS 2015.
In their own words: students and academics write about academic integrity

We report on a survey of Australian computing students and academics that was designed to explore their thoughts about academic integrity with regard to the assessments undertaken in computing degrees. A number of questions on the survey permitted free-text responses, and we have conducted a qualitative analysis of those responses to identify concerns that were not covered in the quantitative part of the survey and to uncover new perspectives on issues that were covered in the survey. In response to specific questions, we identified a perception that copying program code without reference can be legitimate; a perception that copying of program code cannot be detected because all correct answers will effectively be the same; and some suggestions, possibly hitherto unreported, as to why students might engage in academic misconduct. In response to a completely open question, we identified four themes, concerning the implementation and the applicability of academic integrity policy and procedure, possible reasons for breaching academic integrity, and justifications for breaching academic integrity. We conclude by discussing what can be done, by universities and by individual academics, to bring the academic discipline of computing closer to consensus with regard to the meaning of academic integrity and its practice in computing assessments.
The Tomato DELLA Protein PROCERA Acts in Guard Cells to Promote Stomatal Closure

The tomato DELLA protein PROCERA, a negative regulator of gibberellin signaling, increases the sensitivity of guard cells to abscisic acid, leading to stomatal closure and increased drought tolerance. Plants employ stomatal closure and reduced growth to avoid water deficiency damage. Reduced levels of the growth-promoting hormone gibberellin (GA) lead to increased tolerance to water deficit, but the underlying mechanism is unknown. Here, we show that the tomato (Solanum lycopersicum) DELLA protein PROCERA (PRO), a negative regulator of GA signaling, acts in guard cells to promote stomatal closure and reduce water loss in response to water deficiency by increasing abscisic acid (ABA) sensitivity. The loss-of-function pro mutant exhibited increased stomatal conductance and rapid wilting under water deficit stress. Transgenic tomato overexpressing constitutively active stable DELLA proteins (S-della) displayed the opposite phenotype. The effects of S-della on stomatal aperture and water loss were strongly suppressed in the ABA-deficient mutant sitiens, indicating that these effects of S-della are ABA dependent. While DELLA had no effect on ABA levels, guard cell ABA responsiveness was increased in S-della and reduced in pro plants compared with the wild type. Expressing S-della under the control of a guard-cell-specific promoter was sufficient to increase stomatal sensitivity to ABA and to reduce water loss under water deficit stress but had no effect on leaf size. This result indicates that DELLA promotes stomatal closure independently of its effect on growth.
Impact of the Pneumococcal Conjugate Vaccine on Pneumococcal Parapneumonic Empyema

Background: Pediatric pneumococcal parapneumonic empyema (PPE) has become increasingly common. In the last decade, Utah has had one of the highest rates of PPE in the United States, 14/100,000 children, attributed primarily to Streptococcus pneumoniae serotype 1. Our objective was to describe the temporal trends in PPE in Utah before and after the availability of the 7-valent pneumococcal conjugate vaccine (PCV-7). Methods: The Intermountain Health Care (IHC) data warehouse was queried for all cases of empyema in children younger than 18 years, defined as International Classification of Diseases, 9th revision, Clinical Modification code 510.9, for the study period March 1996–June 2005. We also retrieved and serotyped all blood and pleural fluid isolates of S. pneumoniae from children younger than 18 years with a diagnosis of PPE at Primary Children's Medical Center (PCMC) between March 1996 and June 2005. The pre-PCV-7 period (PRE) included 57 months (March 1996–December 2000) and the post-PCV-7 period (POST) included 54 months (January 2001–June 2005). Results: We identified 776 cases of pediatric empyema in the IHC system, and 478 (62%) were managed at PCMC. In the years 1996–2000, we managed a mean of 38 cases of empyema per year compared with 71.5 cases per year between 2001 and 2004 (P = 0.006). At PCMC, there were 295 cases of invasive pneumococcal disease (IPD), and 74 (25%) were PPE. During the PRE period, PPE represented 24 of 137 (17.5%) cases of IPD compared with 50 of 158 (32%) in the POST period (P = 0.008). One-half of the children with PPE required intensive care and 4 died. During the PRE and POST periods, PPE was most often caused by serotype 1 (46 and 34%, respectively), but in the POST period serogroups 3 (20%), and 19A (14%) were also prevalent. PPE in PCV-7-immunized children was caused exclusively by nonvaccine serotypes. Conclusions: PPE in the post-PCV-7 era is more common, representing one-third of the IPD in children in UT. PPE is associated with significant morbidity and mortality. Serotype 1 remains the most common cause of PPE, but serotypes 3 and 19A are emerging.
Mortality During the First 24 Months After Delivery in Relation to CD4 T-Lymphocyte Levels and Viral Load in a Cohort of Breast-Feeding HIV-1-Infected Women in Dar es Salaam, Tanzania

The objective of this study was to analyze the mortality during the first 24 months after delivery in relation to CD4 T-lymphocyte levels and viral load at enrollment (36 weeks of gestation) in a cohort of HIV-1-seropositive breast-feeding women at the Dar es Salaam site of the multicenter Petra trial (a mother-to-child HIV-1 transmission intervention trial using antiretroviral therapy). Antiretroviral treatment was not available in this setting apart from the short treatment given within the trial around delivery to prevent mother-to-child transmission of HIV. T-lymphocyte subsets were determined by flow cytometry. Plasma HIV-1 RNA was quantified by the Amplicor HIV-1 RNA Monitor v 1.5 assay. Mortality after delivery was analyzed using the life-table technique and Cox regression. The analysis included 266 mothers. The CD4 cell counts at enrollment were <200 cells/mm3 in 14.5% of the mothers. The viral load at enrollment was >100,000 RNA copies/mL in 33.6% of the mothers. The mortality 24 months after delivery was 6.7% (95% CI = 3.1-10.1%). The mortality 24 months after delivery was 29.9% (95% CI = 13.1-46.9%) for mothers with <200 CD4 cells/mm3 at enrollment, 3.3% (95% CI = 0-6.6%) for mothers with 200-499 CD4 cells/mm3, 2.9% (95% CI = 0-7.1%) for mothers with >500 CD4 cells/mm3 (P = 0.0000), 15.0% (95% CI = 6.6-23.4%) for mothers with viral load >100,000 copies/mL at enrollment, and 2.8% (95% CI = 0-5.6%) for mothers with viral load <100,000 copies/mL (P = 0.0000). In the multivariate analysis CD4 cell counts and viral load were both independent risk factors for mortality (P < 0.001 and P = 0.004, respectively). In conclusion, the mortality was high among women with severe immunosuppression or high viral load at enrollment, but not in the rest of the women. CD4 lymphocyte count in late pregnancy was a better predictor of death within 2 years than was viral load. The results support the World Health Organization recommendation to initiate antiretroviral treatment in resource-limited settings in HIV-1-infected adults with CD4 cell counts <200/mm3 and show that this is appropriate also among perinatal women.
Compulsion or chronobiology? A case of severe obsessive-compulsive disorder treated with cognitive-behavioral therapy augmented with chronotherapy.

OBJECTIVES Individuals with treatment-resistant obsessive compulsive disorder (OCD) have elevated rates of delayed sleep phase. This report describes a patient with severe OCD who had failed prior trials of pharmacotherapy and psychotherapy, and whose symptoms were associated with delayed bedtimes and delays in the time she initiated her nighttime compulsions. METHODS Case report. RESULTS A 54 year-old woman with OCD kept sleep/symptom logs as an adjunct to traditional cognitive-behavioral therapy for OCD. At presentation, she reported habitual bedtime = 06:00, wake time = 13:00, sleep latency ' 5 min, and total sleep time = 6.5-7.5 h. Later time of initiating her compulsions was associated with longer time performing the compulsions (r = 0.86, p < 0.001). Cognitive-behavioral therapy with adjunctive chronotherapy was associated with substantial improvement. CONCLUSIONS OCD patients with nighttime compulsions may receive light exposure that results in delayed sleep times/circadian phase. Chronotherapy may enhance outcomes for refractory OCD patients, particularly those who perform compulsions at night.
Pricing American Options With Jumps in Asset and Volatility

Jump risk plays an important role in current financial markets, yet it is a risk that cannot be easily measured and hedged. We numerically evaluate American call options under stochastic volatility, stochastic interest rates and jumps in both the asset price and volatility. By employing the Method of Lines (Meyer (2015)), the option price, the early exercise boundary and the Greeks are computed as part of the solution, which makes the numerical implementation time efficient. We conduct a numerical study to gauge the impact of jumps and stochastic interest rates on American call option prices and on their free boundaries. Jumps tend to increase the values of OTM and ATM options while decreasing the value of ITM options. The option delta is affected in a similar way. The impact of jumps on the free boundary is substantial and depends on the time to maturity. Near expiry, including asset jumps lowers the free boundary and the option holder is more likely to exercise the option, whilst including asset-volatility jumps elevates the free boundary and the option holder is less likely to exercise the option. This relation reverses at the beginning of the options life. The volatility, interest rates and their volatilities have a positive impact on the free boundaries and the option holder is less likely to exercise as these parameters increase.
Criminal Liability of Political Parties in the General Election of Regional Head in Indonesia

Regional Election of 171 (one hundred and seventy-one) regions in Indonesia on 27 June 2018 can be correlated with legislative elections and the election of the President and Vice President of Indonesia in 2019. Candidates for Regional Election are carried by political parties that will later follow the elections in 2019, so that for the Political Party election results are able to show its strength in the region. Regional Election can also be used by Political Parties as one of the ways to achieve victory in General Election 2019. Therefore, Political Parties will mobilize the power and efforts to win in Regional Election. There are many efforts which implemented in negative way and can lead to the criminal act of Regional Election. With regard to the form of associations and administrative structures of Political Parties consisting of centers and regions, this paper traces the criminal liability of political parties to criminal acts of Regional Election. Keywords— Political Parties, Criminal Acts of Regional Election, Criminal Liability
Comparison of Metabolic Abnormalities and Clinical Lipodystrophy 48 Weeks After Switching from HAART to Trizivir™ Versus Continued HAART: The Trizal Study

Abstract Purpose: To analyze the evolution of clinical lipodystrophy (LD) and metabolic abnormalities in patients continuing to receive HAART versus patients switched to Trizivir™ (zidovudine, lamivudine, abacavir) after 48 weeks. Method: Patients treated with HAART >6 months with plasma HIV-1 RNA viral load (VL) <;400 copies/mL and <;50 copies/mL at screening were randomly assigned to continue HAART (103 patients) or to receive Trizivir™ (106 patients). Clinical LD was evaluated using a standardized patient questionnaire only at baseline, weeks 4 and 8, and then every 8 weeks until Week 48. Laboratory evaluation was performed every 4 weeks. Results: The proportion of patients exhibiting ≥1 LD symptom at baseline was 40% in the Trizivir™ arm and 50% in HAART arm (difference not significant). After 48 weeks, the prevalence was 28% and 42% respectively (p = .03), and the median number of LD symptoms per patient was 2 in the Trizivir™ arm and 4 in the continued HAART arm (p = .016). Median decreases in cholesterol levels over the 48-week study period were greater in the Trizivir. arm than in the continued HAART arm (–0.80 vs. –0.44 mmol/L; p < .001). Median triglyceride levels decreased in the Trizivir™ arm but increased in the continued HAART arm (–0.17 and +0.01 mmol/L; p = .006). Suppression of VL was maintained in most patients with no differences between the two arms. Conclusion: A switch from "standard" HAART to Trizivir™ was associated with an improvement in clinical LD and blood lipid abnormalities after 48 weeks.
Freely faceted classification for Web-based information retrieval

In free classification, each concept is expressed by a constant notation, and classmarks are formed by free combinations of them, allowing the retrieval of records from a database by searching any of the component concepts. A refinement of free classification is freely faceted classification, where notation can include facets, expressing the kind of relations held between the concepts. The Integrative Level Classification project aims at testing free and freely faceted classification by applying them to small bibliographical samples in various domains. A sample, called the Dandelion Bibliography of Facet Analysis, is described here. Experience was gained using this system to classify 300 specialized papers dealing with facet analysis itself recorded on a MySQL database and building a Web interface exploiting freely faceted notation. The interface is written in PHP and uses string functions to process the queries and to yield relevant results selected and ordered according to the principles of integrative levels.
A phase I/II study of neoadjuvant liposomal doxorubicin, paclitaxel, and hyperthermia in locally advanced breast cancer

Purpose: The prognosis for locally advanced breast cancer (LABC) patients continues to be poor, with an estimated five-year survival of only 50–60%. Preclinical data demonstrates enhanced therapeutic efficacy with liposomal encapsulation of doxorubicin combined with hyperthermia (HT). Therefore this phase I/II study was designed to evaluate the safety and efficacy of a novel neoadjuvant combination treatment of paclitaxel, liposomal doxorubicin, and hyperthermia. Materials and methods: Eligible patients received four cycles of neoadjuvant liposomal doxorubicin (30–75 mg/m2), paclitaxel (100–175 mg/m2), and hyperthermia. They subsequently underwent either a modified radical mastectomy or lumpectomy with axillary node dissection followed by radiation therapy and then eight cycles of CMF (cyclophosphamide, methotrexate, 5-fluorouracil) chemotherapy. Results: Forty-seven patients with stage IIB-III LABC were enrolled and 43 patients were evaluable. Fourteen patients (33%) had inflammatory breast cancer. Combined (partial + complete) clinical response rate was 72% and combined pathological response rate was 60%. Four patients achieved a pathologically complete response. Sixteen patients were eligible for breast-conserving surgery. The cumulative equivalent minutes (CEM 43) at T90 (tenth percentile of temperature distribution) was significantly greater for those with a pathological response. Four-year disease-free survival was 63% (95% CI, 46%–76%) and the four-year overall survival was 75% (95% CI, 58–86%). Conclusions: Neoadjuvant therapy using paclitaxel, liposomal doxorubicin and hyperthermia is a feasible and well tolerated treatment strategy in patients with LABC. The thermal dose parameter CEM 43 T90 was significantly correlated with attaining a pathological response.
Correction of off resonance‐related distortion in echo‐planar imaging using EPI‐based field maps

We present, here, a simple method for measurement and correction of off‐resonance related geometric distortion in echo‐planar imaging (EP1). This method uses high signal‐to‐noise ratio (SNR) EPI‐based field maps, rapidly acquired using a series of gradient recalled images collected across a range of TE values. This field map is distorted in the same manner as the EPI images to be unwarped, providing a direct look‐up table for the correct location of each pixel of data. This method adds very little scan time and is robust and easy to implement.
Memantine for the Treatment of Phantom Limb Pain: A Systematic Review

ABSTRACT Phantom limb pain (PLP) occurs in up to 85% of patients who have undergone an amputation and remains difficult to treat. Memantine is a N-Methyl-d-aspartate receptor antagonist that has shown benefit in pain syndromes. The objective of this systematic review is to evaluate the evidence for the use of memantine in the treatment of acute and chronic PLP. MEDLINE (1956 to May 2016) and Embase (1957 to May 2016) were queried for articles that characterized the clinical outcomes of patient(s) treated with memantine for PLP. The initial search identified 185 studies and case reports. After screening, eight articles were included. One prospective study, a case report, and two case series demonstrated benefit with memantine in the treatment of acute PLP. However, in chronic PLP that persisted for over 1 year, four prospective studies failed to demonstrate significant analgesic effects with memantine. Memantine was well tolerated in all studies. Memantine appears to be a reasonable option to trial in a patient with a recent amputation or who has failed or cannot tolerate other analgesics. Additional research is needed to further determine the role of memantine in the treatment and prevention of PLP and to identify the population most likely to gain benefit.
Influence of mechanical stress and surface interaction on the aggregation of Aspergillus niger conidia

Productivity of fungal cultures is closely linked with their morphologic development. Morphogenesis of coagulating filamentous fungi, like Aspergillus niger, starts with aggregation of conidia, also denominated as spores. Several parameters are presumed to control this event, but little is known about their mode of action. Rational process optimization requires models that mirror the underlying reaction mechanisms. An approach in this regard is suggested and supported by experimental data. Aggregation kinetics was examined for the first 15 h of cultivation under different cultivation conditions. Mechanical stress was considered as well as pH‐dependent surface interaction. Deliberations were based on a two‐step aggregation mechanism. The first aggregation step is only affected by the pH‐value, not by the fluid dynamic conditions in the bioreactor. The second aggregation step, in contrast, depends on the pH‐value as well as on agitation and aeration induced power input. For the given experimental set‐up, agitation had much more influence than aeration. In addition, hyphal growth rate was determined to be the driving force for the second aggregation step. © 2005 Wiley Periodicals, Inc.