Miracle-dz/UniFAR-FTUs huggingface dataset:
UCD in agile projects: dream team or odd couple?

i n t e r a c t i o n s / n o v e m b e r + d e c e m b e r 2 0 0 5 IMAGINE INTERVIEWING for the position of UCD specialist in a company that uses an agile software development process. Could you answer questions such as, “how does UCD fit in an agile process? ” UCD specialists may be horrified when they first hear about agile methods [1]. Agile literature emphasizes developers delivering production code quickly rather performing extensive analysis and design (e.g., UCD) prior to coding. However, the agile literature indicates that this perception is simplistic and misguided. Examining professional practice, as we do in this article, paints a different picture of how UCD and agile practices coexist in a development team.
Biomarker Discovery from We to Me: Is Learning from Each Patient a New Approach?

The immune response is a dynamic multistep process with a complex system regulation. Identification of predictive biomarkers is therefore challenging. Deep investigation of an exceptional responder to pembrolizumab in ovarian cancer identifies a new mechanism of response and highlights the interest of individualized medicine strategy. Clin Cancer Res; 24(14); 3233–5. ©2018 AACR. See related article by Bellone et al., p. 3282
A Naturally Occurring Mutation in ropB Suppresses SpeB Expression and Reduces M1T1 Group A Streptococcal Systemic Virulence

Epidemiological studies of group A streptococcus (GAS) have noted an inverse relationship between SpeB expression and invasive disease. However, the role of SpeB in the course of infection is still unclear. In this study we utilize a SpeB-negative M1T1 clinical isolate, 5628, with a naturally occurring mutation in the gene encoding the regulator RopB, to elucidate the role of RopB and SpeB in systemic virulence. Allelic exchange mutagenesis was used to replace the mutated ropB allele in 5628 with the intact allele from the well characterized isolate 5448. The inverse allelic exchange was also performed to replace the intact ropB in 5448 with the mutated allele from 5628. An intact ropB was found to be essential for SpeB expression. While the ropB mutation was shown to have no effect on hemolysis of RBC's, extracellular DNase activity or survival in the presence of neutrophils, strains with the mutated ropB allele were less virulent in murine systemic models of infection. An isogenic SpeB knockout strain containing an intact RopB showed similarly reduced virulence. Microarray analysis found genes of the SpeB operon to be the primary target of RopB regulation. These data show that an intact RopB and efficient SpeB production are necessary for systemic infection with GAS.
Regulation of intracellular heme trafficking revealed by subcellular reporters

Significance The intracellular and extracellular trafficking of heme, a hydrophobic and potentially cytotoxic cofactor in proteins such as hemoglobin, remains an underexplored area. While cellular heme can be derived exogenously or from de novo synthesis, it is unclear if there is differential trafficking of heme from these two sources. To critically examine this possibility, we developed peroxidase-based enzymatic reporters for heme and deployed them in subcellular compartments in mammalian cells and in several tissues in the Caenorhabditis elegans animal model. Our results show that extracellular and endogenous heme is trafficked to virtually all intracellular compartments via distinct cellular routes and that interorgan heme transport is essential for systemic regulation of heme homeostasis in C. elegans. Heme is an essential prosthetic group in proteins that reside in virtually every subcellular compartment performing diverse biological functions. Irrespective of whether heme is synthesized in the mitochondria or imported from the environment, this hydrophobic and potentially toxic metalloporphyrin has to be trafficked across membrane barriers, a concept heretofore poorly understood. Here we show, using subcellular-targeted, genetically encoded hemoprotein peroxidase reporters, that both extracellular and endogenous heme contribute to cellular labile heme and that extracellular heme can be transported and used in toto by hemoproteins in all six subcellular compartments examined. The reporters are robust, show large signal-to-background ratio, and provide sufficient range to detect changes in intracellular labile heme. Restoration of reporter activity by heme is organelle-specific, with the Golgi and endoplasmic reticulum being important sites for both exogenous and endogenous heme trafficking. Expression of peroxidase reporters in Caenorhabditis elegans shows that environmental heme influences labile heme in a tissue-dependent manner; reporter activity in the intestine shows a linear increase compared with muscle or hypodermis, with the lowest heme threshold in neurons. Our results demonstrate that the trafficking pathways for exogenous and endogenous heme are distinct, with intrinsic preference for specific subcellular compartments. We anticipate our results will serve as a heuristic paradigm for more sophisticated studies on heme trafficking in cellular and whole-animal models.
An adaptive group lasso based multi-label regression approach for facial expression analysis

In the realm of facial expression analysis, numerous attempts have been made to link each facial picture to one affective category. Nevertheless, in our daily life, few of the facial expressions are exactly one of the predefined affective states. Therefore, to analyze the facial expressions more effectively, this paper proposes an Adaptive Group Lasso based Multilabel Regression approach, which depicts each facial expression with multiple continuous values of predefined affective states. Adaptive Group Lasso is adopted to depict the relationship between different labels which different facial expressions share some same affective facial areas (patches). Moreover, to solve the multi-label regression problem, a convex optimization formulation is presented, which would guarantee a global optimal solution. The experiment results based on JAFFE dataset have verified the superior performance of our approach.
Using Visualisation Techniques to Acquire a Better Understanding of Storytelling for Cultural Heritage

Historical information has an important role regarding cultural heritage. It is used to interpret facts occurred in the past and also to understand the present. Storytelling, when applied in the narrative of true events and resulting from different personal views and anecdotal stories, act as an important source of historical information. In this paper, we discuss the problems we encounter in the field of historical information storytelling and we present a software architecture to facilitate the comprehension of stories. More precisely, the proposed solution helps to analyse a story, examine its composition identifying existing entity classes and computing possible relations with other stories, to finally build a visual representation of these stories.
Defining and Predicting Early Recurrence in 957 Patients With Resected Pancreatic Ductal Adenocarcinoma.

OBJECTIVES To establish an evidence-based cutoff to differentiate between early and late recurrence and to compare clinicopathologic risk factors between the two groups. SUMMARY BACKGROUND DATA A clear definition of "early recurrence" after pancreatic ductal adenocarcinoma resection is currently lacking. METHODS Patients undergoing pancreatectomy for pancreatic ductal adenocarcinoma between 2000 and 2013 were included. Exclusion criteria were neoadjuvant therapy and incomplete follow-up. A minimum P-value approach was used to evaluate the optimal cut-off value of recurrence-free survival to divide the patients into early and late recurrence cohorts based on subsequent prognosis. Potential risk factors for early recurrence were assessed with logistic regression models. RESULTS Of 957 included patients, 204 (21.3%) were recurrence-free at last follow-up. The optimal length of recurrence-free survival to distinguish between early (n = 388, 51.5%) and late recurrence (n = 365, 48.5%) was 12 months (P < 0.001). Patients with early recurrence had 1-, and 2-year post-recurrence survival rates of 20 and 6% compared with 45 and 22% for the late recurrence group (both P < 0.001). Preoperative risk factors for early recurrence included a Charlson age-comorbidity index ≥4 (OR 1.65), tumor size > 3.0 cm on computed tomography (OR 1.53) and CA 19-9 > 210 U/mL (OR 2.30). Postoperative risk factors consisted of poor tumor differentiation grade (OR 1.66), microscopic lymphovascular invasion (OR 1.70), a lymph node ratio > 0.2 (OR 2.49), and CA 19-9 > 37 U/mL (OR 3.38). Adjuvant chemotherapy (OR 0.28) and chemoradiotherapy (OR 0.29) were associated with a reduced likelihood of early recurrence. CONCLUSION A recurrence-free interval of 12 months is the optimal threshold for differentiating between early and late recurrence, based on subsequent prognosis.
Comparison of Hemodynamic Responses Associated with Tracheal Intubation Under Various Induction Doses of Remifentanil and Propofol

Background: The optimal dose of propofol and remifentanil induction to minimize the cardiovascular response associated with tracheal intubation may exist. We investigated the cardiovascular response associated with tracheal intubation when various continuous induction doses of remifentanil in combination with propofol were used. Methods: Seventy- five patients were randomly allocated into 1 of 3 groups: the R-0.4 P-1 group (remifentanil 0.4 μg/kg/min and propofol 1 mg/kg); the R-0.5 P-1 group (remifentanil 0.5 μg/kg/min and propofol 1 mg/kg); and the R-0.4 P-2 group (remifentanil 0.4 μg/kg/min and propofol 2 mg/kg). One minute after remifentanil infusion commenced, a bolus of propofol was injected. Rocuronium 1 mg/kg was administered 1 min after propofol injection following loss of consciousness. Controlled ventilation was then performed for 2 min, and the trachea was intubated 4 min after the start of the remifentanil infusion. The infusion rate of remifentanil was decreased to 0.1 μg/kg/min after intubation. Blood pressure (BP) and heart rate (HR) were measured during this period until 5 min after tracheal intubation. Results: The changes in BP response due to tracheal intubation in the R-0.4 P-1 group were greater than those in the other 2 groups, whereas the HR responses to tracheal intubation were similar among the 3 groups. Conclusion: The combination of remifentanil 0.4 μg/kg/min and propofol 1 mg/kg led to an exaggerated cardiovascular response to tracheal intubation compared with the other combination groups.
Extraction and Characterization of Chick PEA (Cicer arietinum) Extract with Immunostimulant Activity in BALB/C MICE

Traditional plant medicines are used for a range of cancer conditions. The chickpea is highly proteinaceous and consumed as a staple in many parts of the world. An evaluation of chemoprotective and immunomodulatory activities of Cicer arietinum (CE) in cisplatin-induced immunosuppressed mice was here performed. Cisplatin was given at 100mg/kg, intraperitoneally, and after induction of immunosuppression mice were treated with Cicer arietinum (0.5 mg/dose/animal/IP) for a period of 10-day. The influence of the extract on lymphoid organ weight, bone marrow cellularity, alpha esterase activity and on enzyme levels such as (SGOT, SGPT, Urea, Creatinine was assessed to identify any chemoprotective influence. Administration of CE to cisplatin-treated mice alleviated the drastic reduction in bone marrow cellularity and α- esterase positive cells seen with cisplatin. Thus myelosuppression was reversed or inhibited. Cisplatin bids to DNA and causes damage resulting in chromosome breaks, micronucleus formation and cell death. CE is comprised of numerous middle-chain aliphatic alcohols, aldehydes and ketones, in addition to compounds like 7-hydroxy-1-methoxy-6-methylanthraquinone, cyclohexadecane (CAS) and 6-(amino methyl)-2-naphthol. These latter are thought to contribute to the characteristic aroma of C. arietimnum. In conclusion, administration of CE in cisplatin-treated mice, boosted bone marrow cellularity and increased α- esterase positive cells, thus reversing myelosupproession.
Study of Casting Parameters and Magnesium Effects on the Distribution of Boride Particles during Centrifugal Casting of functionally graded Aluminum Matrix Composite

An experimental investigation of the effect of casting parameters during the fabrication of functionally graded Al-BMg (Al-2 wt. % B6 wt. % Mg) composites via centrifugal casting method has been conducted. Particular interest was dedicated to the transformation of the dodecaboride particles into complex aluminum diboride particles and the redistribution of these particles on the matrix of the composites. Pertinent image analysis permitted characterizing the resulting composite microstructures both quantitatively and qualitatively. Our results revealed that as casting time, rotational speed and pouring temperature of the melt increased, the concentration of the reinforcement particles becomes denser at the outer periphery of the casting. The data obtained from both superficial Rockwell hardness and Vickers microhardness analysis demonstrated that both mechanical properties bore similar trend as the gradient in particles distribution. Additionally, backscattered electron imaging helped differentiate the morphology and apparent composition of the aluminum boride particles with different levels of boron. The interaction of the magnesium levels in the composite matrix and the reinforcement particles via energy dispersive spectroscopy is also discussed.
Nanocellulose Films from Amazon Forest Wood Wastes: Structural and Thermal Properties

The aim of this work was to determine the best fibrillation intensity that should be used to produce high crystalline and thermal stable microfibrillated cellulose (MFC) and nanocellulose films from C. goeldiana veneer wastes. The number of passages (cycles) of cellulose suspension tested in grinder were 10, 20, 30 and 40. Important properties to be analyzed included changes in morphology from the raw wood to the nanocellulose films, increases/decreases in cellulose crystalline index for inference on biomaterial strength, and thermal behavior changes to support conclusions on biomaterials processing and application possibilities. After chemical treatments for cellulose isolation, mechanical shearing was applied to produce cellulose nanostructures; hence nanocellulose films could be successfully produced from C. goeldiana wood wastes. Influence of more refining cycles on thermal properties, indicated higher stability for 40-cycles nanocellulose films. In general, grinder refining process decreased crystalline index of cellulose.
PRIS in TREC 2008 Blog Track

This paper describes BUPT (pris) participation in baseline adhoc retrieval task and the opinion retrieval task at Blog Track 2008. The system adopts a two-stage strategy in the opinion retrieval task. In the first stage, the system carries out a basic topic relevance retrieval to get the top 1,000 documents for each query. In the second stage, our system combines several Maximum Entropy based classifiers to implement opinion judging and ranking.
Brain structural changes in patients in the early stages of multiple sclerosis with depression

Abstract Some studies suggest an inflammatory mechanism associated with the presence of depression in multiple sclerosis (MS); however, there is little data concerning these findings. The purpose of this study was to investigate the presence of brain structural changes in patients with MS and depression and to compare them with patients suffering from MS without depression and healthy controls. Methods: A case-control study that included patients with relapsing-remitting MS (RRMS) defined by validated criteria, over 18 years of age, with less than three years from disease onset, EDSS ≤ 3, with no history of previous depression and under immunomodulatory treatment with interferon beta, if any. A control group paired by age and gender was also included. Patients were clinically assessed to determine the presence of depression. Demographic clinical and structural aspects of parameters from the scan, such as lesion volume, total brain volume (TBV), white matter volume (WMV), neocortical gray matter volume (NGMV), and fractional anisotropy (FA) were analyzed. Results: Sixty-five individuals were enrolled: 20 healthy controls, 22 patients with MS without depression, and 23 patients with MS with depression. Patients with MS and depression showed a lower TBV (P = 0.01), NGMV (0.01) together with an increase in lesion burden in T2 (P < 0.01) but not in T1 (P = 0.09) and no differences in global FA among groups (P = 0.23) and in WMV (P = 0.12). Conclusion: Patients with RRMS and depression had a reduced total brain volume and a significantly increased lesion burden at T2 MR than patients with RRMS without depression.
Reproductive and gynecologic care of women with fragile X primary ovarian insufficiency (FXPOI)

Objective:Approximately 20% of women with a premutation in the FMR1 gene experience primary ovarian insufficiency (POI). We explored diagnostic patterns, frequency of appropriate hormone replacement, obstetric outcomes, fertility treatment, reproductive decisions, and counseling of women with fragile X-associated POI (FXPOI). Methods:Semistructured interviews with 79 women with FXPOI were conducted by a single interviewer. FMR1 cytosine-guanine-guanine repeat size was determined from a blood, saliva, or buccal sample. Results:The median age of POI onset for women in our study was 33 years. Seventy-two percent of the women had an FMR1 cytosine-guanine-guanine repeat length of 80 to 100. Mean length of time from symptom onset to POI diagnosis was 1.12 years, longer in women with a younger age of POI onset and shorter in women who knew they were carriers. After diagnosis, 52% of women never took hormone therapy, started it years after POI diagnosis, or stopped it before 45 years of age. Forty-nine percent of the women had infertility, but 75% had had at least one genetically related child. Obstetric outcomes were similar to the general population. Forty-six percent of women had a diagnosis of low bone mineral density or osteoporosis, and an additional 19% had never had a bone density assessment. Conclusions:Women with FXPOI are at significant risk for delayed POI diagnosis and undertreatment with hormone therapy. Although approximately 50% of women had infertility, most were able to conceive at least one child and had no elevated risk of adverse obstetric outcomes.
A Survey on Databases for Facial Expression Analysis

Facial expression databases are essential to develop and test a system of facial expressions analysis. We propose in this paper a survey based on the review of 61 databases. To the best of our knowledge, there are no other surveys with so many databases. We identify 18 characteristics to describe the database and group them in 6 categories, (population, modalities, data acquisition hardware, experimental conditions, experimental protocol and annotations). These characteristics are useful to create or choose a database relevant to the targeted context application. We propose to classify the databases according to these characteristics so it can be helpful for researchers to choose the database suited to their context application. We bring to light the trends between posed, spontaneous and in-the-wild databases. We finish with future directions, including crowd sourcing and databases with groups of people.
Dissipation of double‐stranded RNA in aquatic microcosms

Silencing genes of a pest with double‐stranded RNA (dsRNA) is a promising new pest management technology. As part of the environmental risk assessment for dsRNA‐based products, the environmental fate and the potential for adverse effects to on‐target organisms should be characterized. In the present study, a nonbioactive dsRNA was spiked into the water column of a water and sediment microcosm to mimic drift from a spray application run off of unbound dsRNA or transport of plant tissues. Dissipation of dsRNA in the water column and partitioning into sediment was determined. The dsRNA rapidly dissipated in the water column and was below the limit of detection after 96 h. The levels detected in the sediment were not significant and may indicate rapid degradation in the water column prior to partitioning to sediment. Environ Toxicol Chem 2017;36:1249–1253. © 2016 SETAC
Preparation of Laser Frequency Tripling Antireflective Film with High-strength

Nano-porous SiO2 antireflective film with high-strength was made using dipping-coating technique with ammonia process post treatment by Sol-Gel method. The effect of different dip speed on transmission spectra is studied. The result shows that the site of transmission peak shifts with various dip speed. After ammonia process treatment, the mechanical property of film was improved obviously and the mechanism was discussed by IR spectrum,AFM analysis methods. Laser frequency tripling antireflective film was made on silex glass substrate. The reflectance of film at 355 run is about 99.58% .
Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites

NADH (NAD+) and its reduced form NADH serve as cofactors for a variety of oxidoreductases that participate in many metabolic pathways. NAD+ also is used as substrate by ADP-ribosyl transferases and by sirtuins. NAD+ biosynthesis is one of the most fundamental biochemical pathways in nature, and the ubiquitous NAD+ synthetase (NadE) catalyzes the final step in this biosynthetic route. Two different classes of NadE have been described to date: dimeric single-domain ammonium-dependent NadENH3 and octameric glutamine-dependent NadEGln, and the presence of multiple NadE isoforms is relatively common in prokaryotes. Here, we identified a novel dimeric group of NadEGln in bacteria. Substrate preferences and structural analyses suggested that dimeric NadEGln enzymes may constitute evolutionary intermediates between dimeric NadENH3 and octameric NadEGln. The characterization of additional NadE isoforms in the diazotrophic bacterium Azospirillum brasilense along with the determination of intracellular glutamine levels in response to an ammonium shock led us to propose a model in which these different NadE isoforms became active accordingly to the availability of nitrogen. These data may explain the selective pressures that support the coexistence of multiple isoforms of NadE in some prokaryotes.