Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating the NRCS Runoff Curve Number in Delineation of Hydrologic Homogeneous Regions

Cluster analysis, the generally used technique in delineation of hydrologic homogeneous regions for regional flood frequency analysis, requires standardization of flood governing attributes, and hence makes use of large subjective consideration. A new technique is developed for the delineation with no need of standardizing the attributes. The technique uses Natural Resources Conservation Services runoff curve number as a starting point in proposing the hydrologic regions. Five numbers of hydrologic regions were proposed inside the Nepalese territory by superimposing monsoon rainfall map over the runoff curve number map. The L -moment based regional hydrologic homogeneity test led finalization of hydrologic regions with minor adjustments. Heterogeneity measure value, which is a regional homogeneity test parameter representing dispersion in sample moment coefficients among the basins, was found within or near acceptable limit in each of the region. The use of the regionalization for estimating extreme flood.
Neural correlates of the spacing effect in explicit verbal semantic encoding support the deficient‐processing theory

Spaced presentations of to‐be‐learned items during encoding leads to superior long‐term retention over massed presentations. Despite over a century of research, the psychological and neural basis of this spacing effect however is still under investigation. To test the hypotheses that the spacing effect results either from reduction in encoding‐related verbal maintenance rehearsal in massed relative to spaced presentations (deficient processing hypothesis) or from greater encoding‐related elaborative rehearsal of relational information in spaced relative to massed presentations (encoding variability hypothesis), we designed a vocabulary learning experiment in which subjects encoded paired‐associates, each composed of a known word paired with a novel word, in both spaced and massed conditions during functional magnetic resonance imaging. As expected, recall performance in delayed cued‐recall tests was significantly better for spaced over massed conditions. Analysis of brain activity during encoding revealed that the left frontal operculum, known to be involved in encoding via verbal maintenance rehearsal, was associated with greater performance‐related increased activity in the spaced relative to massed condition. Consistent with the deficient processing hypothesis, a significant decrease in activity with subsequent episodes of presentation was found in the frontal operculum for the massed but not the spaced condition. Our results suggest that the spacing effect is mediated by activity in the frontal operculum, presumably by encoding‐related increased verbal maintenance rehearsal, which facilitates binding of phonological and word level verbal information for transfer into long‐term memory. Hum Brain Mapp, 2010. © 2009 Wiley‐Liss, Inc.
The Global Diffusion of Ideas

We provide a tractable, quantitatively‐oriented theory of innovation and technology diffusion to explore the role of international trade in the process of development. We model innovation and diffusion as a process involving the combination of new ideas with insights from other industries or countries. We provide conditions under which each country's equilibrium frontier of knowledge converges to a Fréchet distribution, and derive a system of differential equations describing the evolution of the scale parameters of these distributions, that is, countries' stocks of knowledge. The model remains tractable with many asymmetric countries and generates a rich set of predictions about how the level and composition of trade affect countries' frontiers of knowledge. We use the framework to quantify the contribution of bilateral trade costs to long‐run changes in TFP and individual post‐war growth miracles. For our preferred calibration, we find that both gains from trade and the fraction of variation of TFP growth accounted for by changes in trade more than double relative to a model without diffusion.
Coordinated regulation of extracellular matrix synthesis by the microRNA-29 family in the trabecular meshwork.

PURPOSE The microRNA-29 (miR-29) family has emerged, in various tissues, as a key modulator of extracellular matrix (ECM) homeostasis. In this study, the authors investigate the role of the miR-29 family in the regulation of ECM synthesis in the trabecular meshwork (TM) under basal and TGF-β2 stimulatory conditions. METHODS Human TM cells were incubated with 2.5 ng/mL activated, recombinant human TGF-β2 for 24, 48, and 72 hours. A specific pharmacologic inhibitor was used to block SMAD3 function in the context of TGF-β2 stimulation. Changes in the expression of the miR-29 family were assessed by real-time PCR. The effect of miR-29 molecules and inhibitors on ECM levels was determined by immunoblot analysis. RESULTS All three members of the miR-29 family were expressed in cultured TM cells. Although the incubation of TM cells with TGF-β2 induced miR-29a and suppressed miR-29b levels, no significant effect was observed on miR-29c expression. Additional studies revealed that SMAD3 modulates miR-29b expression under basal and TGF-β2 conditions. Subsequent gain- and loss-of-function experiments demonstrated that the miR-29 family functions as a critical suppressor of various ECM proteins under basal and TGF-β2 stimulatory conditions. CONCLUSIONS The findings derived from this study identify the miR-29 family as a critical regulator of ECM expression in the TM and suggest that its modulation by TGF-β2 may be important in controlling ECM synthesis. Together, these data provide further insight into the complex regulatory mechanisms mediating TGF-β2 signaling and ECM production in the TM.
Discovery of a ciliate parasitoid of euphausiids off Oregon, USA: Collinia oregonensis n. sp. (Apostomatida: Colliniidae).

An apostome ciliate, Collinia oregonensis n. sp. , is reported inhabiting the cephalothorax and abdomen of 3 euphausiid species from the Oregon-Washington coast: Euphausia pacifica Hansen, 1911, Thysanoessa spinifera Holmes, 1900, and Thysanoessa gregaria G.O. Sars, 1883. This ciliate is the 7th species described for the genus Collinia and the 2nd species known to infect euphausiids. Disease progression and ciliate morphology are described using (1) modified protargol stain, (2) hematoxylin counterstained with Fast Green, and (3) Scanning Electron Microscopy (SEM). All endoparasitic developmental stages (trophont, tomont, tomitogenesis, protomite, and tomite) of C. oregonensis are astomatous and possess between 14 and 22 kineties. C. oregonensis is smaller than C. beringensis Capriulo & Small, 1986, which infects the euphausiid Thysanoessa inermis Krøyer, 1846 in the Bering Sea and which possesses between 24 and 80 kineties. The ciliate is a parasitoid because it must kill the host to complete its life cycle. Infections and mortalities in multiple host species likely reflect the virulent nature of the ciliate. Adult euphausiids infected with this parasitoid possess a swollen and bright orange cephalothorax. C. oregonensis feeds and proliferates inside euphausiids, producing fulminating infections that rupture the cephalothorax and release large numbers of tomites into the surrounding water. After several hours in the free swimming stage under shipboard conditions in the present study, the tomites adhered to each other, forming filaments. Infection rates ranged between 3 and 20% within individual euphausiid aggregations, but infected aggregations were randomly and sparingly distributed. Infected euphausiids were found at 6.7% of 316 stations sampled during 3 summer cruises. No infected euphausiids were collected in winter. Because E. pacifica and T. spinifera account for about 90% of the euphausiid standing stock in the northern California Current System, this parasitoid ciliate may have a significant impact on euphausiid population abundance, distribution and secondary productivity.
Software Development Environments for Scientific and Engineering Software: A Series of Case Studies

The need for high performance computing applications for computational science and engineering projects is growing rapidly, yet there have been few detailed studies of the software engineering process used for these applications. The DARPA High Productivity Computing Systems Program has sponsored a series of case studies of representative computational science and engineering projects to identify the steps involved in developing such applications (i.e. the life cycle, the workflows, technical challenges, and organizational challenges). Secondary goals were to characterize tool usage and identify enhancements that would increase the programmers' productivity. Finally, these studies were designed to develop a set of lessons learned that can be transferred to the general computational science and engineering community to improve the software engineering process used for their applications. Nine lessons learned from five representative projects are presented, along with their software engineering implications, to provide insight into the software development environments in this domain.
Determinants of Salt Sensitivity in Black and White Normotensive and Hypertensive Women

Abstract—Salt sensitivity (SS) has been linked to human hypertension. We examined ethnic differences in the relation between SS; erythrocyte sodium (Na+i), calcium (Ca2+i), potassium (K+i), and magnesium (Mg2+i); and sodium pump activity in African-American (AA) and white women. In a crossover protocol, similar numbers of normotensive, hypertensive, AA, and white women were randomized to 7 days of a 20 meq/d and a >200 meq/d salt diet (n=199). After an overnight inpatient stay, group differences in supine blood pressure (BP), heart rate, erythrocyte cations, and sodium pump activity were measured. The prevalence of SS (53.5% vs 51%) and salt resistance (26.3% vs 30.0%) was similar in both races. Greater mean BP increase with salt loading was seen in AA vs white hypertensives but not between the normotensive women. In hypertensives, increase in mean arterial pressure was 12.6 vs 8.2 mm Hg in AAs vs whites, respectively (P <0.01), and for systolic BP, it was 23 vs 14.8 mm Hg (P <0.01). Higher Na+i and Ca2+i were noted in SS and salt-intermediate AA than in the corresponding white subjects. Na+i, Ca2+i, and the ratios of Na+i to K+i and of Ca2+i to Mg2+i were positively correlated with salt responsiveness in AA but not in white women. Sodium pump activity was similar between groups, although the change in maximal activity trended to vary inversely with SS in AA. In closely matched AA and white women, the prevalence of SS is similarly high in both races, although the magnitude of BP increase is greater in AA hypertensives. In AA but not in whites, SS is positively associated with Na+i, Ca2+i, and the ratios of Na+i to K+i and of Ca2+i to Mg2+i.
Seasonal nutrient depletion and carbon export in the Subantarctic and Polar Frontal zones of the Southern Ocean south of Australia

Seasonal surface water nitrate and phosphate depletions were calculated for the Subantarctic Zone (SAZ) and Polar Frontal Zone (PFZ) of the Southern Ocean along the World Ocean Circulation Experiment SR3 repeat section south of Tasmania, Australia, and three other transects slightly to the west. The depletions were calculated between a single winter (July) section and eight other sections from October to March in the years 1991-1998 and corrected for frontal movements and changes in water masses between the cruises using observed quasi-linear nutrient-salinity relationships. Arranged in a seasonal progression, depletion began in approximately October and continued through March, in good agreement with satellite biomass-based estimates of production. Nitrate depletion in the SAZ (510 mmol N m−2) was approximately twice that of the PFZ (250 mmol N m−2), but phosphate depletions were similar (29 and 24 mmol P m−2 for the SAZ and PFZ, respectively). The SAZ exhibited a Redfield N/P depletion ratio (15.1±2.3), but the PFZ ratio was much lower (8.3±5.4). While the SAZ exhibits greater seasonal nutrient depletion, the relative magnitudes of export in the two zones remain uncertain because supply of nutrients from south of the Polar Front may lower the observed nutrient depletions in the PFZ. However, comparisons with sediment trap and production measurements for the region south of Australia suggest the SAZ and PFZ differences derive from differences in production. Assuming a Redfield C/N ratio (6.6), carbon export for the longest period examined (July-March) averaged 3400±430 mmol C m−2 in the SAZ, with a range between 2700 and 3900 mmol C m−2 depending on latitude. In the PFZ, carbon export averaged 1600±350 mmol C m−2, with a range of 1100 to 2000 mmol C m−2. These averages represent minimum annual export production estimates because neither resupply nor export outside the July-March observational period is included.
The Gut Mucosal Viral Reservoir in HIV-Infected Patients Is Not the Major Source of Rebound Plasma Viremia following Interruption of Highly Active Antiretroviral Therapy

ABSTRACT Interruption of suppressive highly active antiretroviral therapy (HAART) in HIV-infected patients leads to increased HIV replication and viral rebound in peripheral blood. Effects of therapy interruption on gut-associated lymphoid tissue (GALT) have not been well investigated. We evaluated longitudinal changes in viral replication and emergence of viral variants in the context of T cell homeostasis and gene expression in GALT of three HIV-positive patients who initiated HAART during primary HIV infection but opted to interrupt therapy thereafter. Longitudinal viral sequence analysis revealed that a stable proviral reservoir was established in GALT during primary HIV infection that persisted through early HAART and post-therapy interruption. Proviral variants in GALT and peripheral blood mononuclear cells (PBMCs) displayed low levels of genomic diversity at all times. A rapid increase in viral loads with a modest decline of CD4+ T cells in peripheral blood was observed, while gut mucosal CD4+ T cell loss was severe following HAART interruption. This was accompanied by increased mucosal gene expression regulating interferon (IFN)-mediated antiviral responses and immune activation, a profile similar to those found in HAART-naive HIV-infected patients. Sequence analysis of rebound virus suggested that GALT was not the major contributor to the postinterruption plasma viremia nor were GALT HIV reservoirs rapidly replaced by HIV rebound variants. Our data suggest an early establishment and persistence of viral reservoirs in GALT with minimal diversity. Early detection of and therapy for HIV infection may be beneficial in controlling viral evolution and limiting establishment of diverse viral reservoirs in the mucosal compartment.
Atherothrombotic Middle Cerebral Artery Territory Infarction: Topographic Diversity With Common Occurrence of Concomitant Small Cortical and Subcortical Infarcts

Background and Purpose MRI has superior capabilities for the detection of cerebral infarcts compared with CT. CT was used to locate infarcts in most previous studies of atherothrombotic middle cerebral artery (MCA) territory infarcts. Thus, there was a possibility of missing concomitant small infarcts. More accurate identification of topographic lesions in MCA territory with MRI may help to establish the pathogenesis of stroke. The present study determines topographic patterns, distribution of vascular lesions, and probable mechanisms. Methods Forty-two patients with MCA territory infarcts on routine MRI and no major cause of cardioembolism were studied with conventional angiography or MR angiography. Results The topographic patterns seen on MRI were subdivided into 4 groups: cortical border-zone infarcts (n=6), pial territory infarcts without insular infarct (n=3), pial territory infarcts with insular infarct (n=14), and large subcortical infarcts (n=19). Of 6 patients with cortical border-zone infarcts, 4 had concomitant small cortical or subcortical multiple lesions. Angiography showed intrinsic MCA disease in 4 patients. Of 3 patients with pial territory infarcts without insular infarct, 2 also had small multiple centrum ovale lesions. All had intrinsic MCA disease. Pial territory infarcts with partial or whole insular lesions were present in 10 and 4 patients, respectively. Five patients had additional multiple cortical or subcortical lesions. Ten patients had intrinsic MCA disease. Of the 19 patients with large subcortical infarcts, 12 had centrum ovale infarcts, and 4 had both basal ganglia and centrum ovale lesions. Ten had concomitant small cortical or subcortical lesions. Six patients had intrinsic MCA disease. Conclusions Similar vascular lesions induce different topographic patterns in MCA territory infarction, which are related to individual vascular variability, degree of primary and secondary collateralization, and pathogenesis of infarcts. Our study indicates that concomitant small cortical or subcortical lesions are also commonly associated findings in diverse patterns of MCA territory infarction, which can mostly be explained by probable embolic mechanism.
Pollen and macrofossil evidence of Late Pleistocene and Holocene treeline fluctuations from an alpine lake in Colorado, USA

High-resolution pollen, plant macrofossil and magnetic susceptibility (MS) data are presented from an alpine lake sediment core from west-central Colorado, recording changes in vegetation and sedimentation for the latest Pleistocene and Holocene (c. the last 12.5 ka; 1 ka = 1000 cal. yr BP). During the Younger Dryas chron (c. 12.9–11.5 ka), Artemisia steppe or tundra grew around the lake, but by the earliest Holocene (10.7–9.5 ka) a subalpine Picea and Abies parkland was established there. Picea remained important through the early Holocene, but also bristlecone and lodgepole pines (Pinus aristata and P. contorta) grew around the lake. Warming conditions are indicated from 9.5 ka, lasting until c. 4.5–3.5 ka, which may have been the warmest period, with greatest development of monsoonal conditions. Trees subsequently retreated downslope from Kite Lake c. 150–200 m during the last 3.5 ka, establishing their present treeline position. A decrease in total Pinus and increases in Artemisia and piñon (P. edulis) indicate a trend toward progressive climate cooling and enhanced winter precipitation. These long-term climatic trends correlate with Holocene changes in summer insolation.
Short‐Term Stover, Tillage, and Nitrogen Management Affect Near‐Surface Soil Organic Matter

Corn (Zea mays L.) stover removal for biofuel or forage has implications on soil organic C (SOC). The objective of this study was to evaluate short-term (3-yr) stover management (retained or removed [79% removed, across treatments and years]), tillage system (chisel tillage, strip-tillage, and no-till [CT, ST, and NT, respectively]), and fertilizer N (0 and 224 kg N ha⁻¹) effects on particulate and total soil C and N in continuous corn (CC) cropping systems on fine-textured soils in the Upper Midwest. Soil samples were collected at study initiation in 2008 and at its conclusion in 2011. Stover removal decreased SOC in the surface depth (D1) by 15% compared to when it was retained and 11% when compared with the baseline level. In the same depth, SOC with CT was 10 and 9% less than with ST and NT, respectively, and 10% less than the baseline. Particulate organic matter C (POM-C) decreased in D1 between sampling times with stover removal in all tillage systems. When stover was retained, POM-C in D1 increased 36 and 40% over the baseline with ST and NT, respectively, but decreased 18% with CT. Chisel tillage decreased POM-C in the sampled soil profile by 13 and 17% compared with ST and NT, respectively, and by 21% when compared with the baseline. These results demonstrate that annually harvesting the maximum quantities of stover in CC allowable by field-scale machinery can reduce near-surface particulate and total soil organic matter in the Upper Midwest after 3 yr, but losses can be reduced by tillage systems that reduce soil disturbance.
Stroke Impact Scale-16

Objectives: To 1) develop a short instrument (Stroke Impact Scale–16 [SIS-16]) to assess physical function in patients with stroke at approximately 1 to 3 months poststroke using items from the composite physical domain of the Stroke Impact Scale (SIS) version 3.0, and 2) compare the SIS-16 and a commonly used disability measure, the Barthel Index (BI), in terms of their ability to discriminate disability. Methods: A total of 621 subjects enrolled in the GAIN Americas randomized stroke trial were included in this study. Rasch analysis, which models the probability of a subject’s response to an item using both subject ability and item difficulty, was used to construct the SIS-16, describe its properties, and compare its ordering and range of item difficulties to those of the BI. Box plots and analysis of variance were used to examine differences in BI and SIS-16 scores across modified Rankin categories. Results: The study sample had an average age of 68 ± 12.4 years and 56% were men. Stroke diagnoses were classified as minor in 91 patients (NIH Stroke Scale score [NIHSS] 0 to 5), moderate in 304 (NIHSS 6 to 13), and major in 226 (NIHSS ≥ 14). Twelve of the original 28 items in the SIS version 3.0 composite physical domain were eliminated to produce the SIS-16, with a minimal loss of reliability. As compared to the BI, the SIS-16 contains more difficult items that can differentiate patients with less severe limitations, and therefore has less pronounced ceiling effects. SIS-16 scores were significantly different across Rankin levels 0 to 1, 2, 3, 4, and 5, whereas BI was significantly different only across Rankin levels 0 to 2, 3, 4, and 5. Conclusion: Compared to the BI, the SIS-16 is an excellent collection of items suitable for assessing a wide range of physical function limitations of patients with stroke at 1 to 3 months poststroke. Because of a less pronounced ceiling effect, the SIS-16 can differentiate lower levels of disability as compared to the BI.
Learning user reformulation behavior for query auto-completion

It is crucial for query auto-completion to accurately predict what a user is typing. Given a query prefix and its context (e.g., previous queries), conventional context-aware approaches often produce relevant queries to the context. The purpose of this paper is to investigate the feasibility of exploiting the context to learn user reformulation behavior for boosting prediction performance. We first conduct an in-depth analysis of how the users reformulate their queries. Based on the analysis, we propose a supervised approach to query auto-completion, where three kinds of reformulation-related features are considered, including term-level, query-level and session-level features. These features carefully capture how the users change preceding queries along the query sessions. Extensive experiments have been conducted on the large-scale query log of a commercial search engine. The experimental results demonstrate a significant improvement over 4 competitive baselines.