Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative outcomes of oncologic therapy in gastric extranodal marginal zone (MALT) lymphoma: analysis of the SEER-Medicare database.

BACKGROUND Therapy for gastric marginal zone (MALT) lymphoma is largely based on single-arm trials. This observational study compared survival with radiotherapy, rituximab and combination chemoimmunotherapy in this disease. PATIENTS AND METHODS Gastric MALT lymphoma cases diagnosed between 1997 and 2007 were selected from the Surveillance, Epidemiology and End Results-Medicare database. Propensity score analysis and competing risk models were used to compare survival in patients with stage IE treated with radiation or chemotherapy, and in patients of all stages treated with rituximab alone or with chemoimmunotherapy. RESULTS Among 1134 patients, 21% underwent radiation and 24% chemotherapy as initial treatment. In the balanced cohort of 347 patients with stage IE, radiotherapy alone was associated with a better cause-specific survival [hazard ratio (HR) 0.27, P < 0.001]. Patients receiving systemic therapy had better survival if it incorporated rituximab (HR 0.53, P = 0.017). After adjustment for confounding, the outcomes of those who received rituximab alone or combination chemoimmunotherapy were not statistically different (P = 0.14). CONCLUSIONS In elderly patients with stage IE gastric MALT lymphoma, radiotherapy was associated with lower risk of lymphoma-related death than chemotherapy. In those requiring systemic treatment, addition of cytotoxic chemotherapy to rituximab in the first-line regimen was not associated with improved survival.
Structure and Physicochemical Properties of Nitrogenated Derivatives of Cellulose

Nitrogenated derivatives of cellulose, and namely chitin and chitosan, are of commercial interest because of their antibacterial activity, biocompatibility, biodegradability and sorption ability. Structure and some physicochemical properties of these derivatives have been studied by methods of wide-angle X-ray scattering (WAXS), microcalorimetry and sorption. To determine the crystallinity degree of the samples, an improved WAXS method was used based on the calculation of the relationship between integrated intensities of X-ray diffraction from crystalline and amorphous domains. The calculations revealed that the actual degree of crystallinity of initial chitin was 0.72, and of initial chitosan 0.57. After ball-grinding for a short time, the decrease in the crystallinity degree was observed, whereas the prolonged grinding resulted in complete amorphization of the samples. The wetting enthalpy and sorption ability of the samples were inversely proportional to degree of crystallinity. Reduction of the crystallinity degree of the samples promoted increasing of the wetting enthalpy and water sorption. This evidences that mechanism of interaction between the nitrogenated polysaccharides and water is absorption of the water molecules into amorphous domains of the hydrophilic polymers. The crystallinity degree values calculated from results of water vapor sorption and wetting enthalpy were close to the crystallinity degree of the samples obtained by the WAXS method.
Selection Constrains High Rates of Tandem Repetitive DNA Mutation in Daphnia pulex

Tandemly repeated DNA is known to be highly abundant and highly divergent between species, but the genome-wide mutation rates in these mostly unmappable. A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here, we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex, in addition to six isolates from a non-MA population originating from the same progenitor, to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual repeats were both high and highly variable, ranging from additions/deletions of 0.29–105 copies per generation (reflecting changes of 0.12–0.80% per generation). Our results also provide evidence that new repeat sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33% lower variation in repeat copy number on average than the MA lines, although the level of selective constraint was not evenly distributed across all repeats. The changes between many pairs of repeats were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that tandem repeats can experience extremely rapid evolution in copy number, which can lead to high levels of divergence in genome-wide repeat composition between closely related species.
Improved product‐per‐glucose yields in P450‐dependent propane biotransformations using engineered Escherichia coli

P450‐dependent biotransformations in Escherichia coli are attractive for the selective oxidation of organic molecules using mild and sustainable procedures. The overall efficiency of these processes, however, relies on how effectively the NAD(P)H cofactors derived from oxidation of the carbon source are utilized inside the cell to support the heterologous P450‐catalyzed reaction. In this work, we investigate the use of metabolic and protein engineering to enhance the product‐per‐glucose yield (YPPG) in whole‐cell reactions involving a proficient NADPH‐dependent P450 propane monooxygenase prepared by directed evolution [P450PMOR2; Fasan et al. (2007); Angew Chem Int Ed 46:8414–8418]. Our studies revealed that the metabolism of E. coli (W3110) is able to support only a modest propanol:glucose molar ratio (YPPG ∼ 0.5) under aerobic, non‐growing conditions. By altering key processes involved in NAD(P)H metabolism of the host, considerable improvements of this ratio could be achieved. A metabolically engineered E. coli strain featuring partial inactivation of the endogenous respiratory chain (Δndh) combined with removal of two fermentation pathways (ΔadhE, Δldh) provided the highest YPPG (1.71) among the strains investigated, enabling a 230% more efficient utilization of the energy source (glucose) in the propane biotransformation compared to the native E. coli strain. Using an engineered P450PMOR2 variant which can utilize NADPH and NADH with equal efficiency, we also established that dual cofactor specificity of the P450 enzyme can provide an appreciable improvement in YPPG. Kinetic analyses suggest, however, that much more favorable parameters (KM, kcat) for the NADH‐driven reaction are required to effectively compete with the host's endogenous NADH‐utilizing enzymes. Overall, the metabolic/protein engineering strategies described here can be of general value for improving the performance of NAD(P)H‐dependent whole‐cell biotransformations in E. coli. Biotechnol. Bioeng. 2011; 108:500–510. © 2010 Wiley Periodicals, Inc.
Credibility and the Dynamics of Collective Attention

Today, social media provide the means by which billions of people experience news and events happening around the world. However, the absence of traditional journalistic gatekeeping allows information to flow unencumbered through these platforms, often raising questions of veracity and credibility of the reported information. Here we ask: How do the dynamics of collective attention directed toward an event reported on social media vary with its perceived credibility? By examining the first large-scale, systematically tracked credibility database of public Twitter messages (47M messages corresponding to 1,138 real-world events over a period of three months), we established a relationship between the temporal dynamics of events reported on social media and their associated level of credibility judgments. Representing collective attention by the aggregate temporal signatures of an event's reportage, we found that the amount of continued attention focused on an event provides information about its associated levels of perceived credibility. Events exhibiting sustained, intermittent bursts of attention were found to be associated with lower levels of perceived credibility. In other words, as more people showed interest during moments of transient collective attention, the associated uncertainty surrounding these events also increased.
Projections from the ventral cochlear nucleus to the dorsal cochlear nucleus in rats

Local circuit interactions between the dorsal and ventral divisions of the cochlear nucleus are known to influence the evoked responses of the resident neurons to sound. In the present study, we examined the projections of neurons in the ventral cochlear nucleus to the dorsal cochlear nucleus by using retrograde transport of biotinylated dextran amine injected into restricted but different regions of the dorsal cochlear nucleus. In all cases, we found retrogradely labeled granule, unipolar brush, and chestnut cells in the granule cell domain, and retrogradely labeled multipolar cells in the magnocellular core of the ventral cochlear nucleus. A small number of the labeled multipolar cells were found along the margins of the ventral cochlear nucleus, usually near the boundaries of the granule cell domain. Spherical bushy, globular bushy, and octopus cells were not labeled. Retrogradely‐labeled auditory nerve fibers and the majority of labeled multipolar neurons formed a narrow sheet extending across the medial‐to‐lateral extent of the ventral cochlear nucleus whose dorsoventral position was topographically related to the injection site. Labeled multipolar cells within the core of the ventral cochlear nucleus could be divided into at least two distinct groups. Planar neurons were most numerous, their somata found within the associated band of labeled fibers, and their dendrites oriented within this band. This arrangement mimics the organization of isofrequency contours and implies that planar neurons respond best to a narrow range of frequencies. In contrast, radiate neurons were infrequent, found scattered throughout the ventral cochlear nucleus, and had long dendrites oriented perpendicular to the isofrequency contours. This dendritic orientation suggests that radiate neurons are sensitive to a broad range of frequencies. These structural differences between planar and radiate neurons suggest that they subserve separate functions in acoustic processing. J. Comp. Neurol. 385:245–264, 1997. © 1997 Wiley‐Liss, Inc.
On the equivalence of blind equalizers based on MRE and subspace intersections

Two classes of algorithms for multichannel blind equalization are the mutually referenced equalizer (MRE) method by Gesbert et al. (see ibid. vol.45, p.2307-17, 1997) and the subspace intersection (SSI) method by van der Veen et al. (see ibid., vol. 45, no.1, p.173-90, 1997). Although these methods seem, at first sight, unrelated, we show that certain variants of the SSI and the MRE methods both optimize a new blind criterion, which is referred to as maximum coherence and, thus, are equivalent.
Activation, homing, and role of the mesenchymal stem cells in the inflammatory environment

Human mesenchymal stem cells (MSCs) are considered to be a promising source of cells in regenerative medicine. They have large potential to differentiate into various tissue-specific populations and may be isolated from diverse tissues in desired quantities. As cells of potential autologous origin, they allow recipients to avoid the alloantigen responses. They also have the ability to create immunomodulatory microenvironment, and thus help to minimize organ damage caused by the inflammation and cells activated by the immune system. Our knowledge about the reparative, regenerative, and immunomodulatory properties of MSCs is advancing. At present, there is a very comprehensible idea on how MSCs affect the immune system, particularly in relation to the tissue and organ damage on immunological basis. Hitherto a number of effective mechanisms have been described by which MSCs influence the immune responses. These mechanisms include a secretion of soluble bioactive agents, an induction of regulatory T cells, modulation of tolerogenic dendritic cells, as well as induction of anergy and apoptosis. MSCs are thus able to influence both innate and adaptive immune responses. Soluble factors that are released into local microenvironment with their subsequent paracrine effects are keys to the activation. As a result, activated MSCs contribute to the restoration of damaged tissues or organs through various mechanisms facilitating reparative and regenerative processes as well as through immunomodulation itself and differentiation into the cells of the target tissue.
Taste and food preferences as predictors of dietary practices in young women

Abstract Objective: To investigate links between taste responses, self-reported food preferences and selected dietary outcomes in young women. Methods: Subjects were 159 women, with a mean age of 27.0 years. Taste responses were measured using aqueous solutions of 6−n-propylthiouracil (PROP) and sucrose. All subjects completed a 171-item food preference checklist, using nine-point category scales. Food preference data were reduced using principal components factor analyses, with the internal consistency of factor-based subscales established using Cronbach's alpha. Dietary intakes, available for a subset of 87 women, were based on 3 days of food records. Estimated intakes of carbohydrate, fibre and β-carotene were the key dietary outcome variables. Results: Genetically-mediated sensitivity to the bitter taste of PROP was associated with reduced preferences for Brussels sprouts, cabbage, spinach and coffee beverages. Higher preferences for sucrose in water were associated with increased preferences for sweet desserts. Food preferences, in turn, were associated with measures of current diet. Reduced acceptability of vegetables and fruits was associated with lower estimated intakes of carbohydrate, fibre and β-carotene. Conclusions: Taste responses to sucrose and PROP were predictive of some food preferences. Food preferences, in turn, were associated with food consumption patterns. Given that taste responsiveness to PROP is an inherited trait, there may be further links between genetic taste markers, eating habits and the selection of healthful diets.
“ Decomposition of changes in the consumption of

Vietnam is undergoing a nutritional transition like many middle-income countries. This paper proposes to highlight the socio-demographic drivers of this transition over the period 2004-2014. We implement a method of decomposition of between-year differences in economic outcomes recently proposed in the literature. This method allows decomposing the composition effect on the distribution of the outcome under study, which is due to the differences in covariates across years, into direct contributions of each covariate and effects of their interactions. This method is applied to VHLSS data. The results show the importance of between-year changes in the distributions of covariates on between-year changes in the distributions of total calorie intake and calorie intakes from proteins and fat. This effect is more contrasted in case of calorie intake from carbohydrates. Food expenditure and household size appear to be the main drivers of the observed evolutions in macronutrients consumption. On the contrary, the urbanization of the population has a negative effect on these evolutions, except on fat consumption. The effect of urbanization is, nevertheless, less important than the positive effects of the previous two variables.
Methylphenidate treatment of adult male prison inmates with attention-deficit hyperactivity disorder: randomised double-blind placebo-controlled trial with open-label extension

Background Attention-deficit hyperactivity disorder (ADHD) is highly prevalent in prison inmates, but pharmacological treatment has not yet been evaluated in this group. Aims To evaluate osmotic-release oral system (OROS) methylphenidate in adult male long-term prison inmates with ADHD. Method Randomised, double-blind, placebo-controlled 5-week trial, followed by 47-week open-label extension in 30 prison inmates with ADHD and comorbid disorders. Primary outcome was level of ADHD symptoms after 5 weeks, evaluated by a masked assessor. Secondary outcomes were self-reported ADHD symptoms, global severity and global functioning throughout the 52-week trial, and post hoc treatment response and numbers needed to treat (NNT) (trial registration: NCT00482313.) Results Treatment significantly improved ADHD during the trial (P<0.001; Cohen's d = 2.17), with reduced symptom severity and improved global functioning. The placebo response, cardiovascular measures and adverse events were non-significant; the NNT was 1.1. Attention-deficit hyperactivity disorder symptoms, global severity and global functioning continued to improve during the open-label extension. Conclusions Osmotic-release oral system methylphenidate is an effective treatment for adult male prison inmates with ADHD.
Toward Improved Daily Cloud-Free Fractional Snow Cover Mapping with Multi-Source Remote Sensing Data in China

With the high resolution of optical data and the lack of weather effects of passive microwave data, we developed an algorithm to map daily cloud-free fractional snow cover (FSC) based on the Moderate Resolution Imaging Spectroradiometer (MODIS) standard daily FSC product, the Advanced Microwave Scanning Radiometer (AMSR2) snow water equivalent (SWE) product and digital elevation data. We then used the algorithm to produce a daily cloud-free FSC product with a resolution of 500 m for regions in China. In addition, we produced a high-resolution FSC map using a Landsat 8 Operational Land Imager (OLI) image as a true value to test the accuracy of the cloud-free FSC product developed in this study. The analysis results show that the daily cloud-free FSC product developed in this study can completely remove clouds and effectively improve the accuracy of snow area monitoring. Compared to the true value, the mean absolute error of our product is 0.20, and its root mean square error is 0.29. Thus, the synthesized product in this study can improve the accuracy of snow area monitoring, and the obtained snow area data can be used as reliable input parameters for hydrological and climate models. The land cover type and terrain factors are the main factors that limit the accuracy of the daily cloud-free FSC product developed in this study. These limitations can be further improved by improving the accuracy of the MODIS standard snow product for complicated underlying surfaces.
Gemcitabine and oxaliplatin for metastatic pancreatic adenocarcinoma: a North Central Cancer Treatment Group phase II study.

BACKGROUND This study was performed to determine the efficacy of gemcitabine and oxaliplatin in patients with advanced or metastatic pancreatic adenocarcinoma (ACA). PATIENTS AND METHODS Pancreatic ACA patients with previously untreated advanced or metastatic disease were enrolled in a phase II study of gemcitabine and oxaliplatin. Oxaliplatin was given i.v. on day 1 and gemcitabine i.v. on days 1 and 8 of a 3-week cycle. The primary end point of the trial was 6-month survival. Secondary end points included response rate, overall survival, median time to progression and toxicity. RESULTS A total of 47 patients were enrolled, 46 of whom were evaluable. Of those patients assessed for the primary end point 50% lived for > or =6 months. The median time to progression was 4.53 months. Five confirmed responses were seen with a median duration of response of 2.7 months. Overall, the treatment was well tolerated. However, one patient died as a result of treatment-related hemolytic uremic syndrome. CONCLUSIONS Gemcitabine and oxaliplatin, at doses of 1000 mg/m(2) and 100 mg/m(2), respectively, showed moderate activity in patients with pancreatic ACA. Based on the results of this study further evaluation of this combination is warranted.
Sacred forests of India: a strong tradition of community-based natural resource management

SUMMARY Sacred forests represent an important long-held tradition of conserving specific land areas that have cultural, and often religious, significance. India, with its diversity of cultures and traditions, has over 100 000 sacred forests. Many of these groves are forest fragments in agricultural landscapes. In most cases, community members are at least aware of these fragments, if not actively involved in their protection and management. This review focuses on the Western Ghats in southern India and Meghalaya state in north-eastern India, both international biodiversity hotspots. In addition to the cultural significance of sacred forests, a number of studies have suggested that they are important refuges for conservation of biological diversity, including medicinal plants, within highly anthropogenic landscapes. Whilst sacred groves have been successful conservation areas, current threats to these forests are numerous, ranging from pressures for use of timber and other forest products to clearing for agriculture or general changes in cultural traditions. A variety of arrangements exist for ownership and management of sacred forests, making it necessary to identify solutions on a case-by-case basis. Support for the continued practice of the tradition of sacred forest protection is needed in order to provide a culturally sensitive model for community-based natural resource management.
Neurochemistry of Idiopathic Restless Legs Syndrome

The pathogenesis of idiopathic restless legs syndrome (iRLS) is not well established, but the most important hypothesis suggests dopaminergic dysfunction and iron deficiency. However, recent reports suggest a possible role for several neurotransmitters or neuromodulators, such as aspartate, glutamate, gamma-hydroxybutyric acid (GABA) and opiates, as well as relation with vitamin D deficiency. In this review, we summarise the studies related to neurochemical findings in iRLS.
Comparative Study of the Epidemiology of Rotavirus in Children from a Community-Based Birth Cohort and a Hospital in South India

ABSTRACT Rotavirus gastroenteritis is the major cause of severe dehydrating diarrhea in children worldwide. This study compares rotavirus diarrhea in 351 children in a community-based cohort and 343 children admitted to a hospital during the same period. Clinical information and fecal specimens were obtained during diarrheal episodes. Fecal samples were screened for VP6 antigen, and the positive samples were G and P typed by reverse transcription-PCR. Rotavirus was detected in 82/1,152 (7.1%) episodes of diarrhea in the community and 94/343 (27.4%) cases in the hospital. The median age of affected children (7.5 versus 10.5 months) and the mean severity of symptoms (Vesikari score, 7.6 ± 3.4 versus 11 ± 2.5) were lower in the community. A larger proportion of children in the community were breast-fed than were children admitted to the hospital (73% versus 34.8%). In the community, the genotypes identified in symptomatic patients, in order of frequency, were G1 (36.5%), G10 (17.1%), G2 (15.9%), and G9 (7.3%) and mixed infections (7.3%). The most common G-P combinations were G1P[8], G2P[4], G1P[4], and G10P[11]. The distribution of G types from hospitalized children was G1 (46.8%), G9 (19.1%), G2 (8.5%), G10 (1.1%), and 4.3% mixed infections. The most common G-P combinations were G1P[8] and G9P[8]. This study documents significant genetic heterogeneity of rotaviruses in the community and the hospital. G10P[11] strains resembling a vaccine candidate strain caused disease in the community, indicating the need for careful epidemiological studies as well as safety studies for the vaccine candidates.