Miracle-dz/UniFAR-FTUs huggingface dataset:
Streamflow Regime Variations Following Ecological Management on the Loess Plateau, China

The continuous ecological management of the Loess Plateau is known throughout the world for two strategies: the integrated soil conservation project that began in the 1970s, and the “Grain for Green” project that began in the 1990s. Six sub-catchments nested in the Beiluo River basin were selected to investigate streamflow regime variations during the two project periods. The annual streamflow trends and change points were detected using a bootstrap-based Mann-Kendall test and Pettitt test. Annual streamflow (from the 1950s to 2011) exhibited significantly negative trends in five out of six catchments, varying from −0.15 to −0.30 mm/a. During the integrated soil conservation period, the annual streamflow was reduced due to high flow decreases (5% of time exceeded), whereas in the low flows (95%) it increased in all sub-catchments. During the “Grain for Green” period, the annual streamflow decreased due to daily streamflow reductions at four stations. In addition to high flow and low flow decreases at the Wuqi and Liujiahe stations during the “Grain for Green” period, it is significant that the low flows continuously increased. Compared with trends from the forestry area, which includes the Zhangcunyi and Huangling stations, incremental annual streamflow reductions were observed in other sub-catchments, which can be linked to ecological management. This result implies that streamflow can be moderated by appropriate management options, even in semiarid areas. It was concluded that a stable streamflow regime can be achieved in vegetated areas, and streamflow moderation is dependent on ecological management practices.
A Chaperone Function of NO CATALASE ACTIVITY1 Is Required to Maintain Catalase Activity and for Multiple Stress Responses in Arabidopsis

Arabidopsis protein NCA1 interacts with catalases in the cytosol and increases catalase activity through maintaining catalase folding state, which is required for stress responses. Catalases are key regulators of reactive oxygen species homeostasis in plant cells. However, the regulation of catalase activity is not well understood. In this study, we isolated an Arabidopsis thaliana mutant, no catalase activity1-3 (nca1-3) that is hypersensitive to many abiotic stress treatments. The mutated gene was identified by map-based cloning as NCA1, which encodes a protein containing an N-terminal RING-finger domain and a C-terminal tetratricopeptide repeat-like helical domain. NCA1 interacts with and increases catalase activity maximally in a 240-kD complex in planta. In vitro, NCA1 interacts with CATALASE2 (CAT2) in a 1:1 molar ratio, and the NCA1 C terminus is essential for this interaction. CAT2 activity increased 10-fold in the presence of NCA1, and zinc ion binding of the NCA1 N terminus is required for this increase. NCA1 has chaperone protein activity that may maintain the folding of catalase in a functional state. NCA1 is a cytosol-located protein. Expression of NCA1 in the mitochondrion of the nca1-3 mutant does not rescue the abiotic stress phenotypes of the mutant, while expression in the cytosol or peroxisome does. Our results suggest that NCA1 is essential for catalase activity.
Regulation of PGC-1α Isoform Expression in Skeletal Muscles

The coactivator PGC-1α is the key regulator of mitochondrial biogenesis in skeletal muscle. Skeletal muscle expresses several PGC-1α isoforms. This review covers the functional role of PGC-1α isoforms and the regulation of their exercise-associated expression in skeletal muscle. The patterns of PGC-1α mRNA expression may markedly differ at rest and after muscle activity. Different signaling pathways are activated by different physiological stimuli, which regulate the expression of the PGC-1α gene from the canonical and alternative promoters: expression from a canonical (proximal) promoter is regulated by activation of the AMPK; expression from an alternative promoter, via a β2-adrenergic receptor. All transcripts from both promoters are subject to alternative splicing. As a result, truncated isoforms that possess different properties are translated: truncated isoforms are more stable and predominantly activate angiogenesis, whereas full-length isoforms manly regulate mitochondrial biogenesis. The existence of several isoforms partially explains the broad-spectrum function of this protein and allows the organism to adapt to different physiological stimuli. Regulation of the PGC-1α gene expression by different signaling pathways provides ample opportunity for pharmacological influence on the expression of this gene. Those opportunities might be important for the treatment and prevention of various diseases, such as metabolic syndrome and diabetes mellitus. Elucidation of the regulatory mechanisms of the PGC-1α gene expression and their functional role may provide an opportunity to control the expression of different isoforms through exercise and/or pharmacological intervention.
Odor vapor pressure and quality modulate local field potential oscillatory patterns in the olfactory bulb of the anesthetized rat

A central question in chemical senses is the way that odorant molecules are represented in the brain. To date, many studies, when taken together, suggest that structural features of the molecules are represented through a spatio‐temporal pattern of activation in the olfactory bulb (OB), in both glomerular and mitral cell layers. Mitral/tufted cells interact with a large population of inhibitory interneurons resulting in a temporal patterning of bulbar local field potential (LFP) activity. We investigated the possibility that molecular features could determine the temporal pattern of LFP oscillatory activity in the OB. For this purpose, we recorded the LFPs in the OB of urethane‐anesthetized, freely breathing rats in response to series of aliphatic odorants varying subtly in carbon‐chain length or functional group. In concordance with our previous reports, we found that odors evoked oscillatory activity in the LFP signal in both the beta and gamma frequency bands. Analysis of LFP oscillations revealed that, although molecular features have almost no influence on the intrinsic characteristics of LFP oscillations, they influence the temporal patterning of bulbar oscillations. Alcohol family odors rarely evoke gamma oscillations, whereas ester family odors rather induce oscillatory patterns showing beta/gamma alternation. Moreover, for molecules with the same functional group, the probability of gamma occurrence is correlated to the vapor pressure of the odor. The significance of the relation between odorant features and oscillatory regimes along with their functional relevance are discussed.
Online Submission ID : 1072 Visually Validating Expansion Characteristics in Acoustic Hydrothermal Plume Data

Some recent geological findings suggest that hydrothermal plumes may have an impact on the ocean in the same order of magnitude as rivers. One of the distinctive characteristics of plumes is the expansion as they rise into the ocean. The vertical expansion of plumes is visible in photographs, and numerical analysis confirms that it is present in acoustic data. However, it is not apparent in visualizations of the data. This paper presents a study on the ability of several volume rendering methods to convey the presence of such an important characteristic in resultant visualizations. We rendered a number of acoustic plume datasets using isosurface rendering, single-phase direct volume rendering (DVR), and two-phase DVR. We have found that the two-phase DVR method, which is capable of depicting the effects of scattering and shadows in the plume and the surrounding water, is the most effective in showing the presence of vertical expansion of the plume. The results of the two-phase DVR correlate more closely with the numerical analysis of the expansion than the other two methods. In addition, we also implemented a spectral version of two-phase DVR, which depicts the physical characteristics of the plumes using more accurate color and opacity accumulation through the highly interactive medium of underwater particulates. Through this application, we introduces a methodology for validating visualization results through quantitative comparison of expansion characteristics in data and visualization.
DomLock: a new multi-granularity locking technique for hierarchies

We present efficient locking mechanisms for hierarchical data structures. Several applications work on an abstract hierarchy of objects, and a parallel execution on this hierarchy necessitates synchronization across workers operating on different parts of the hierarchy. Existing synchronization mechanisms are either too coarse, too inefficient, or too ad hoc, resulting in reduced or unpredictable amount of concurrency. We propose a new locking approach based on the structural properties of the underlying hierarchy. We show that the developed techniques are efficient even when the hierarchy is an arbitrary graph, and are applicable even when the hierarchy involves mutation. Theoretically, we present our approach as a locking-cost-minimizing instance of a generic algebraic model of synchronization for hierarchical data structures. Using STMBench7, we illustrate considerable reduction in the locking cost, resulting in an average throughput improvement of 42%.
Biaxial Constitutive Modelling and Testing of a Single Crystal Superalloy at Elevated Temperatures

A viscoplastic constitutive model for single crystal superalloys is developed from crystallographic slip theory. The model is applied to the tension and torsion deformation behavior of the single crystal superalloy PWA 1480 at 871 C (1600 F). Both octahedral and cube slip behavior are needed to model the deformation behavior of single crystal superalloys at elevated temperature.
Comparisons and validation of statistical clustering techniques for microarray gene expression data

MOTIVATION With the advent of microarray chip technology, large data sets are emerging containing the simultaneous expression levels of thousands of genes at various time points during a biological process. Biologists are attempting to group genes based on the temporal pattern of their expression levels. While the use of hierarchical clustering (UPGMA) with correlation 'distance' has been the most common in the microarray studies, there are many more choices of clustering algorithms in pattern recognition and statistics literature. At the moment there do not seem to be any clear-cut guidelines regarding the choice of a clustering algorithm to be used for grouping genes based on their expression profiles. RESULTS In this paper, we consider six clustering algorithms (of various flavors! ) and evaluate their performances on a well-known publicly available microarray data set on sporulation of budding yeast and on two simulated data sets. Among other things, we formulate three reasonable validation strategies that can be used with any clustering algorithm when temporal observations or replications are present. We evaluate each of these six clustering methods with these validation measures. While the 'best' method is dependent on the exact validation strategy and the number of clusters to be used, overall Diana appears to be a solid performer. Interestingly, the performance of correlation-based hierarchical clustering and model-based clustering (another method that has been advocated by a number of researchers) appear to be on opposite extremes, depending on what validation measure one employs. Next it is shown that the group means produced by Diana are the closest and those produced by UPGMA are the farthest from a model profile based on a set of hand-picked genes. AVAILABILITY S+ codes for the partial least squares based clustering are available from the authors upon request. All other clustering methods considered have S+ implementation in the library MASS. S+ codes for calculating the validation measures are available from the authors upon request. The sporulation data set is publicly available at http://cmgm.stanford. edu/pbrown/sporulation
Norovirus RNA-Dependent RNA Polymerase Is Phosphorylated by an Important Survival Kinase, Akt

ABSTRACT Viruses commonly use host cell survival mechanisms to their own advantage. We show that Akt, an important signaling kinase involved in cell survival, phosphorylates the RNA-dependent RNA polymerase (RdRp) from norovirus, the major cause of gastroenteritis outbreaks worldwide. The Akt phosphorylation of RdRp appears to be a feature unique to the more prevalent norovirus genotypes such as GII.4 and GII.b. This phosphorylation event occurs at a residue (Thr33) located at the interface where the RdRp finger and thumb domains interact and decreases de novo activity of the polymerase. This finding provides fresh insights into virus-host cell interactions.
Assemblies of organic molecules on insulating surfaces investigated by nc-AFM

The formation of ordered one- and two-dimensional molecular structures on insulating surfaces has been investigated by means of a room temperature scanning force microscope (SFM). In particular, one dimensional row structures along step edges of alkali halide crystals were obtained as well as two dimensional chain structures on the terraces. Various molecules have been deposited on diﬀerent substrates. While most of the combinations didn’t show any ordered structures at all, some combinations led to ordered growth. Porphyrin based molecules have proven to be promising candidates to form self-assembled structures on insulating surfaces. Their close aﬃnity to hemoglobine and chlorophyll makes them also interesting as functional building parts. Porphyrin molecules tend to π − π stack in crystals, allowing them to work as optical or electrical antennae. While the adsorption on metallic surfaces showed that this particular stacking was prevented by the ﬂat alignment on the substrate, molecules were adsorbed standing upright on alkali-halide(100) surfaces maintaining the intermolecular π − π-stacking. Alkali-halide surfaces have been structured in diﬀerent ways to study the molecular arrangements under various conditions. Micrometer long, one dimensional wires along step edges have been observed as well as large two-dimensional assemblies of parallel running wire structures across ﬂat terraces. The orientation of those chains is guided by the underlying substrate and the equilibrium distance between the molecules. In order to check the feasibilty to contact the wires, experiments on gold cluster decorated insulating surfaces have been performed. Under certain premises of the cluster arrangement it proved to be successful to grow molecular wires between two gold clusters. At last, molecular assemblies on ultrathin salt ﬁlms on Cu(111) were studied by means of Kelvin Probe Force Microscopy (KPFM) to obtain details about possible exciton or electron transport in the π − π stacks. The KPFM did not yet show conclusive results, but the dynamic compensation of the contact potential diﬀerence allowed ultrahigh resolution images, which revealed diﬀerences in the adsorption structures on layers of diﬀerent heights. In summary, the adsorption of cyanoporphyrin molecules on various insulation surfaces has been studied and carefully analyzed.
The activity view of inner speech

We distinguish two general approaches to inner speech (IS)—the “format” and the “activity” views—and defend the activity view. The format view grounds the utility of IS on features of the representational format of language, and is related to the thesis that the proper function of IS is to make conscious thinking possible. IS appears typically as a product constituted by representations of phonological features. The view also has implications for the idea that passivity phenomena in cognition may be misattributed IS. The activity view sees IS as a speaking activity that does not have a proper function in cognition. It simply inherits the array of functions of outer speech. We argue that it is methodologically advisable to start from this variety of uses, which suggests commonalities between internal and external activities. The format view has several problems; it has to deny “unsymbolized thinking”; it cannot easily explain how IS makes thoughts available to consciousness, and it cannot explain those uses of IS where its format features apparently play no role. The activity view not only lacks these problems but also has explanatory advantages: construing IS as an activity allows it to be integrally constituted by its content; the view is able to construe unsymbolized thinking as part of a continuum of phenomena that exploit the same mechanisms, and it offers a simple explanation for the variety of uses of IS.
Fetal Fibular Hemimelia

The AIUM Practice Guideline for the Performance of an Antepartum Obstetric Ultrasound Examination 1 recommends documenting the presence or the absence of the fetal extremities during the second trimester of pregnancy. At times both upper and lower extremities may be present, and an obvious fetal malformation may not be apparent until all the long bones are carefully measured and evaluated. This can further be challenging when only 1 limb or part of a limb is affected. In the obstetric literature, there are only a handful of case reports dealing with the prenatal diagnosis of fibular hemimelia (FH; or longitudinal deficiency of the fibula or postaxial hypoplasia of the lower extremity) as an isolated finding or as part of a syndrome.2-9 Typically, it has been diagnosed at birth, when the neonate is seen to have lower limb shortening, a foot deformity (missing 1 or 2 of the lateral toes), or both. However, in the orthopedic literature, there are many case series dealing with the surgical treatment of this entity. We report a case of FH diagnosed prenatally during a "routine" anatomic survey.
Insights into Alternanthera mosaic virus TGB3 Functions: Interactions with Nicotiana benthamiana PsbO Correlate with Chloroplast Vesiculation and Veinal Necrosis Caused by TGB3 Over-Expression

Alternanthera mosaic virus (AltMV) triple gene block 3 (TGB3) protein is involved in viral movement. AltMV TGB3 subcellular localization was previously shown to be distinct from that of Potato virus X (PVX) TGB3, and a chloroplast binding domain identified; veinal necrosis and chloroplast vesiculation were observed in Nicotiana benthamiana when AltMV TGB3 was over-expressed from PVX. Plants with over-expressed TGB3 showed more lethal damage under dark conditions than under light. Yeast-two-hybrid analysis and bimolecular fluorescence complementation (BiFC) reveal that Arabidopsis thaliana PsbO1 has strong interactions with TGB3; N. benthamiana PsbO (NbPsbO) also showed obvious interaction signals with TGB3 through BiFC. These results demonstrate an important role for TGB3 in virus cell-to-cell movement and virus-host plant interactions. The Photosystem II oxygen-evolving complex protein PsbO interaction with TGB3 is presumed to have a crucial role in symptom development and lethal damage under dark conditions. In order to further examine interactions between AtPsbO1, NbPsbO, and TGB3, and to identify the binding domain(s) in TGB3 protein, BiFC assays were performed between AtPsbO1 or NbPsbO and various mutants of TGB3. Interactions with C-terminally deleted TGB3 were significantly weaker than those with wild-type TGB3, and both N-terminally deleted TGB3 and a TGB3 mutant previously shown to lose chloroplast interactions failed to interact detectably with PsbO in BiFC. To gain additional information about TGB3 interactions in AltMV-susceptible plants, we cloned 12 natural AltMV TGB3 sequence variants into a PVX expression vector to examine differences in symptom development in N. benthamiana. Symptom differences were observed on PVX over-expression, with all AltMV TGB3 variants showing more severe symptoms than the WT PVX control, but without obvious correlation to sequence differences.
The Effectiveness of Alternative Monetary Policy Tools in a Zero Lower Bound Environment

This paper reviews alternative options for monetary policy when the short-term interest rate is at the zero lower bound and develops new empirical estimates of the effects of the maturity structure of publicly held debt on the term structure of interest rates. We use a model of risk-averse arbitrageurs to develop measures of how the maturity structure of debt held by the public might affect the pricing of level, slope and curvature term-structure risk. We find these Treasury factors historically were quite helpful for predicting both yields and excess returns over 1990-2007. The historical correlations are consistent with the claim that if in December of 2006, the Fed were to have sold off all its Treasury holdings of less than one-year maturity (about $400 billion) and use the proceeds to retire Treasury debt from the long end, this might have resulted in a 14-basis-point drop in the 10-year rate and an 11-basis-point increase in the 6-month rate. We also develop a description of how the dynamic behavior of the term structure of interest rates changed after hitting the zero lower bound in 2009. Our estimates imply that at the zero lower bound, such a maturity swap would have the same effects as buying $400 billion in long-term maturities outright with newly created reserves, and could reduce the 10-year rate by 13 basis points without raising short-term yields.
Implant surgery using bone- and mucosa-supported stereolithographic guides in totally edentulous jaws: surgical and post-operative outcomes of computer-aided vs. standard techniques.

OBJECTIVES The aim of this study was to compare the surgical and post-operative outcomes of a computer-aided implant surgery performed by bone- and mucosa-supported stereolithographic (SLA) guides against the standard technique. MATERIAL AND METHODS Multiple- and single-type SLA guides from two commercial manufacturers were produced and a total of 341 implants were placed to 52 patients using the standard technique (Control group), bone- (bone-supported guide [BSG] group) and mucosa-supported SLA guides (Flapless group) in 21, 16 and 15 patients, respectively. Surgical duration (min), number of analgesics (tablets) as well as hemorrhage, difficulty in mouth opening (or trismus) and other incidences were recorded. Pain and swelling was assessed using the visual analog scale (VAS). Parametric and non-parametric tests were used for statistical analysis (P<.05). RESULTS The mean surgery duration (23.53+/-5.48 min) and the number of analgesics consumed (four tablets) in the Flapless group were lower than those in the control (68.71+/-11.4 min and 10 tablets) and BSG groups (60.94+/-13.07 min and 11 tablets, P<0.01). The change in pain scores (VAS) and the number of analgesics consumed in time were statistically significant (P<0.01 and 0.05, respectively) and the Flapless group reported a lower pain score than the BSG (P<0.01) and Control groups (P<0.001). The Flapless group experienced less hemorrhage (chi(2)=4.12, P=0.041 on the day of surgery) and fewer instances of trismus (chi(2)=6.91, P=0.031 the day after surgery). The differences in early-term failures were not statistically significant between the groups (log-rank test: P=0.782). CONCLUSION The use of mucosa-supported single SLA guides for flapless implant placement may help reduce the surgery duration, pain intensity, related analgesic consumption and most other complications typical in the post-implant surgery period. However, there are particular drawbacks in both guide types and further studies are required to confirm the prosthodontic conformity and long-term success of implants placed using computer-assisted techniques.