Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the relationship between complexity and performance in a land surface model using the multicriteria method

[1] The performance of five modes of a land surface model, the Chameleon Surface Model (CHASM), was investigated after calibration via the multicriteria method to monthly totals of evaporation and runoff from the Valdai data set. The use of CHASM allows for an exploration into the relationship between surface energy balance complexity and optimal performance by isolating the impacts of different parameterizations of the surface energy balance. When compared to quantities used within the calibration process, CHASM's performance was significantly increased with calibration over default simulations regardless of calibration length or mode complexity. Within the calibration period, CHASM's performance increased with increasing complexity in the representation of the surface energy balance. Outside the calibration period there was little improvement to simulations from additional complexity in the surface energy balance representation above the simplest mode. Calibration is shown to reduce the scatter between modes suggesting that some of the differences between models in PILPS Phase 2d may be explained by the specification of parameter values. For simulations of quantities not used in calibration, performance can be reduced as a result of calibration. This implies that evaporation and runoff may not be the best quantities for calibration in order to improve model performance. It is suggested that the best quantities to calibrate may be mode and model specific.
A parsing machine for PEGs

Parsing Expression Grammar (PEG) is a recognition-based foundation for describing syntax that renewed interest in top-down parsing approaches. Generally, the implementation of PEGs is based on a recursive-descent parser, or uses a memoization algorithm. We present a new approach for implementing PEGs, based on a virtual parsing machine, which is more suitable for pattern matching. Each PEG has a corresponding program that is executed by the parsing machine, and new programs are dynamically created and composed. The virtual machine is embedded in a scripting language and used by a patternmatching tool. We give an operational semantics of PEGs used for pattern matching, then describe our parsing machine and its semantics. We show how to transform PEGs to parsing machine programs, and give a correctness proof of our transformation.
A 2mm2 0.1-to-5GHz SDR receiver in 45nm digital CMOS

The requirements of next-generation wireless terminals are driving RFIC design toward ubiquitous multistandard connectivity at reduced power consumption and cost [1–3]. While the use of scaled CMOS technology is required to allow economically feasible single-chip integration with a digital processor, a Software-Defined Radio (SDR) is the preferred approach to provide a reconfigurable platform, that covers a broad range of noise/linearity specifications while offering the best power/performance trade-off [4,5].
Left Ventricular Mass: Reliability of M-Mode and 2-Dimensional Echocardiographic Formulas

Abstract—The study of left ventricular (LV) hypertrophy is hindered by problems with LV mass measurement by echocardiography. Both the M-mode and 2D area-length formulas for calculating LV mass assume a fixed geometric shape, which may be a source of error. We examined this hypothesis by using cardiovascular magnetic resonance images to eliminate the confounding effects of acoustic access and image quality. LV mass was measured directly in 212 healthy subjects by means of a standard 3D cardiovascular magnetic resonance technique. LV mass was also calculated by using the cube-function and area-length formulas with measurements from the magnetic resonance images. A comparison of serial measurements was made by examining the changes in LV mass by all 3 techniques in those completing an exercise program (n=140). The cube-function technique showed a consistent underestimation of LV mass of 14.3 g, and there were wide 95% limits of agreement (±57.6 g and ±46.3 g for cube-function and area-length techniques, respectively) when compared with 3D measurement. There were similarly wide limits of agreement for the change in mass (±55.2 g and ±44.8 g for cube-function and area-length, respectively). The assumption of geometric shape in the cube-function and area-length formulas resulted in significant variation in LV mass estimates from direct measurement by using a 3D technique. The technique cannot be recommended either at a single time point or for serial studies in small populations; 3D imaging techniques, such as cardiovascular magnetic resonance, are preferable.
Wearable computing meets ubiquitous computing: reaping the best of both worlds

This paper describes what we see as fundamental difficulties in both the pure ubiquitous computing and pure wearable computing paradigms when applied to context-aware applications. In particular, ubiquitous computing and smart room systems tend to have difficulties with privacy and personalization, while wearable systems have trouble with localized information, localized resource control, and resource management between multiple people. These difficulties are discussed and a peer-to-peer network of wearable and ubiquitous computing components is proposed as a solution. This solution is demonstrated through several implemented applications.
Visual identification of software evolution patterns

Software evolution plays a key role in the overall lifecycle of a software system. In this phase, software developers extend the capabilities and functionality of the system to meet new user requirements. However, the maintenance process could rapidly lead to phenomena of "source code deterioration". The possibility to early detect bad software evolution patterns represents a paramount opportunity to keep the application maintainable. In this paper we propose a combined visualization to identify software evolution patterns related to user requirements. Such visualization consists in showing the evolution metrics of a software system together with the implementation of its requirements. We also show some examples on how this visualization could help to identify some "common" evolution patterns.
New drain current model for nano-meter MOS transistors on-chip threshold voltage test

Traditional reliability tests use complicated equipment, like probe stations and semiconductor parameter analyzers, to measure changes in transistors' threshold voltages, which are both expensive and time consuming. This paper provides an idea to test the threshold voltage with existing low-to-moderate accuracy ADCs and DACs inside SoCs. To avoid the low-accuracy limitation of measurement results, a new MOS model for the nano-meter MOS transistor drain current is proposed. This model only uses six parameters and is valid for all regimes, being the sub-threshold/weak-inversion, moderate-inversion, strong-inversion and linear regime. Measurement results from 90nm transistors and simulation results from 65nm BSIM4.6 models are used to validate the new model. Finally, an on-chip threshold test for reliability purpose is proposed and long-time stress measurement for 90nm PMOS transistors are shown.
Protein misfolding in neurodegenerative diseases

A common pathogenic mechanism shared by diverse neurodegenerative disorders, like Alzheimer's disease, Parkinson's disease, Huntington's disease and transmissible spongiform encephalopathies, may be altered protein homeostasis leading to protein misfolding and aggregation of a wide variety of different proteins in the form of insoluble fibrils. Mutations in the genes encoding protein constituents of these aggregates have been linked to the corresponding diseases, thus a reasonable scenario of pathogenesis was based on misfolding of a neurone‐specific protein that forms insoluble fibrils that subsequently kill neuronal cells. However, during the past 5 years accumulating evidence has revealed the neurotoxic role of prefibrillar intermediate forms (soluble oligomers and protofibrils) produced during fibril formation. Many think these may be the predominant neurotoxic species, whereas microscopically visible fibrillar aggregates may not be toxic. Large protein aggregates may rather be simply inactive, or even represent a protective state that sequesters and inactivates toxic oligomers and protofibrils. Further understanding of the biochemical mechanisms involved in protein misfolding and fibrillization may optimize the planning of common therapeutic approaches for neurodegenerative diseases, directed towards reversal of protein misfolding, blockade of protein oligomerization and interference with the action of toxic proteins.
Role of CD8+ Lymphocytes in Control and Clearance of Measles Virus Infection of Rhesus Monkeys

ABSTRACT The creation of an improved vaccine for global measles control will require an understanding of the immune mechanisms of measles virus containment. To assess the role of CD8+ cytotoxic T lymphocytes in measles virus clearance, rhesus monkeys were depleted of CD8+ lymphocytes by monoclonal anti-CD8 antibody infusion and challenged with wild-type measles virus. The CD8+ lymphocyte-depleted animals exhibited a more extensive rash, higher viral loads at the peak of virus replication, and a longer duration of viremia than did the control antibody-treated animals. These findings indicate a central role for CD8+ lymphocytes in the control of measles virus infections and the importance of eliciting a cell-mediated immune response in new measles vaccine strategies.
Concealment and Obstacle Detection for Autonomous Driving

Obstacle detection and mapping are essential for unmanned autonomous driving. This paper describes both the sensors and the supporting software used in our system for driving autonomously on cross-country roads. The Ladar Range Imaging Camera (EBK) is used for monitoring the environment. We describe an algorithm developed at the National Institute of Standards and Technology (NIST) for detecting obstacles and regions of concealment, and evaluate its ability to detect positive (e.g., rocks) and negative (e.g., ditches) obstacles and concealment regions. We discuss the mapping system used for representing general obstacles (positive, negative, and concealment.) In addition to using information provided by the EBK sensor, the mapping algorithm also uses information supplied by a Global Positioning System (GPS) and an Inertial Navigation System (INS). This system has been tested at NIST and has successfully detected obstacles and regions of concealment while driving cross country at speeds of 35 km/h.
Diversity of Helicobacter pylori genotypes in Iranian patients with different gastroduodenal disorders.

AIM To investigate the diversity of Helicobacter pylori (H. pylori) genotypes and correlations with disease outcomes in an Iranian population with different gastroduodenal disorders. METHODS Isolates of H. pylori from patients with different gastroduodenal disorders were analyzed after culture and identification by phenotypic and genotypic methods. Genomic DNA was extracted with the QIAamp DNA mini kit (Qiagen, Germany). After DNA extraction, genotyping was done for cagA, vacA (s and m regions), iceA (iceA1 , iceA2 ) and babA with specific primers for each allele using polymerase chain reaction (PCR). All patients' pathologic and clinical data and their relation with known genotypes were analyzed by using SPSS version 19.0 software. χ² test and Fisher's exact test were used to assess relationships between categorical variables. The level of statistical significance was set at P < 0.05. RESULTS A total of 71 isolates from 177 patients with different gastroduodenal disorders were obtained. Based on analysis of the cagA gene (positive or negative), vacA s-region (s1 or s2), vacA m-region (m1 or m2), iceA allelic type (iceA1 and iceA2 ) and babA gene (positive or negative), twenty different genotypic combinations were recognized. The prevalence of cagA, vacA s1 , vacA s2 , vacA m1 , vacA m2 , iceA1 , iceA2 , iceA1+iceA2 and babA were 62%, 78.9%, 19.7%, 21.1%, 78.9%, 15.5%, 22.5%, 40.8% and 95.8%, respectively. Interestingly, evaluation of PCR results for cagA in 6 patients showed simultaneous existence of cagA variants according to their size diversities that proposed mixed infection in these patients. The most prevalent genotype in cagA-positive isolates was cagA⁺/vacAs1m2 /iceA1 +A2 /babA+ and in cagA-negative isolates was cagA⁻/vacAs1m2 /iceA-/babA+. There were no relationships between the studied genes and histopathological findings (H. pylori density, neutrophil activity, lymphoid aggregation in lamina propria and glandular atrophy). The strains which carry cagA, vacAs1/m1 , iceA2 and babA genes showed significant associations with severe active chronic gastritis (P = 0.011, 0.025, 0.020 and 0.031, respectively). The vacAs1 genotype had significant correlation with the presence of the cagA gene (P = 0.013). Also, babA genotype showed associations with cagA (P = 0.024). In the combined genotypes, only cagA⁺/vacAs1m1 /iceA2 /babA+ genotype showed correlation with severe active chronic gastritis (P = 0.025). CONCLUSION This genotyping panel can be a useful tool for detection of virulent H. pylori isolates and can provide valuable guidance for prediction of the clinical outcomes.
Prebreakup geology of the Gulf of Mexico‐Caribbean: Its relation to Triassic and Jurassic rift systems of the region

A review of the prebreakup geology of west central Pangea, comprising northern South America, the Gulf of Mexico, and West Africa, combined with a study of the Mesozoic rift trends of the region confirms a relation between the rift systems and the underlying older grain of deformation. The prebreakup analysis focuses attention on the Precambrian, early Paleozoic, and late Paleozoic tectonic events affecting the region and assumes a Pindell fit. Two late Precambrian orogenic belts are observed in west central Pangea. Along the northern South American margin and Yucatan a paleo northeast trending Pan-African aged fold belt is documented. A second system is observed along West Africa extending from the High Atlas to the Mauritanides and Rockelides. Similar aged orogenies in the Appalachians are compared. During the late Paleozoic, renewed orogenic activity, associated with the Gondwana-Laurentia suture, affected large segments of west central Pangea. The general trend of the system is northeast-southwest and essentially parallels the Guayana craton and West African and eastern North American cratons. Mesozoic rifling closely followed either the Precambrian trends or the late Paleozoic orogenic belt. The Triassic component focused along the western portions of the Gulf of Mexico continuing into eastern Mexico and western South America. The Jurassic rift trend followed along the separation between Yucatan and northern South America. At Lake Maracaibo the Jurassic rift system eventually overlaps the Triassic rifts. The Jurassic rift resulted in the “Hispanic Corridor” that permitted Tethyan and Pacific marine faunas to mix at a time when the Gulf of Mexico underwent continental sedimentation.
Tumor Suppressors miR-200 c Targets CDK 2 and Suppresses Tumorigenesis in Renal Cell Carcinoma

miRNA expression profiles are widely investigated in the major cancers, but their specific roles and functions in cancers have not yet to be fully elucidated. In this study, miRNA expression profiles were determined in clear cell renal cell carcinomas (ccRCC) and in matched normal kidney tissues by using a miRNA microarray platform which covers a total of 851 human miRNAs. Differential expression of 74 miRNAs were identified between ccRCC specimens and their matched adjacent noncancerous tissues, of which 30 were significantly upregulated in ccRCCs, and the other 44 were downregulated (fold change 2, P < 0.05). Interestingly, miR-200c was commonly downregulated in ccRCC specimens and ccRCC cell lines with significant functional consequences. Growth curve and FACS assay indicated that overexpression of miR-200c suppressed cell growth and induced cell-cycle arrest at G0–G1 phases in SN12-PM6 and 786-O cells. Furthermore, miR-200c could suppress in vivo tumor growth of SN12-PM6 cells in mice. Bioinformatics exposed cyclin-dependent kinase 2 (CDK2) as a potential target of miR-200c, which was validated using a luciferase reporter assay. Mechanistic investigations revealed that miR-200c was directly responsible for suppressing the expression of CDK2 in ccRCC cell lines and xenografts. Taken together, miR-200c plays an antioncogenic role in ccRCC, through controlling cell growth and cell-cycle progression by downregulating the G1–S regulator CDK2. Implications:miR-200c exerts its novel antioncogenic function in renal cell carcinoma by controlling CDK2-dependent cell growth and cell-cycle progression. Mol Cancer Res; 13(12); 1567–77. 2015 AACR.
A satellite-based method for monitoring seasonality in the overstory leaf area index of Siberian larch forest

[1] Reliable monitoring of the leaf area index (LAI) is required to further understand the carbon, water, and energy cycles of forests. In this study, we proposed a new satellite-based method to estimate the overstory LAI (LAIo) separately from the understory LAI (LAIu) for larch forests covering eastern Siberia. We modeled forest scenes representative of larch forest structure, with particular consideration of the typical clumped shoot structure of larch. Three-dimensional radiative transfer simulations were then conducted under various forest conditions to establish the relationships between LAIo and seasonal increases in the normalized difference water index after leaf appearance. Model-based sensitivity analyses indicated a maximum error of up to 26% under known noise levels. Averaged at the continental scale, total LAI from our estimates, the CYCLOPES version 3.1, and the Moderate Resolution Imaging Spectroradiometer MOD15 Collection 5 (main algorithm) showed similar ranges in summer. However, spatial pattern of LAI was slightly different, with smoother variability for CYCLOPES LAI. Our LAI and CYLOPES effective LAI reproduced a realistic seasonal variation with exact timing of spring increase in LAIo. The main drawbacks of MOD15 Collection 5 were unrealistically strong temporal variability, and the fact that LAI began to increase earlier than the overstory leaf appearance date. Overall, the results show that our new method is a good alternative to MOD15 Collection 5 and CYCLOPES, as it provides separate estimates of LAIo and LAIu and true LAI instead of effective LAI.
Five-year monitoring of herpetofauna in Woraksan National Park

In this study, in order to determine how climate change may affect amphibian and reptile communities, we surveyed the numbers of egg clumps and adults of amphibians and the number of reptiles at eight amphibian and nine reptile survey sites in Woraksan National Park from March 2005 to September 2009. We assessed the relationships among six climate factors (annual minimum temperature, annual maximum temperature, monthly mean temperature, monthly mean precipitation, monthly mean temperature during winter, and monthly mean precipitation during winter); species diversity, evenness, and richness indexes for both amphibians and reptiles; and the number of each species and egg clumps of three amphibian species. First, both the amphibian and reptile species indices evidenced sudden changes in 2007, when climate factors in Korea fluctuated substantially. Second, amphibian diversity and evenness were negatively related with annual minimum temperature. Increased monthly mean precipitation had a positive effect in mountain edge sites, but a negative effect in valley sites. Third, reptile species evenness was positively related with monthly mean precipitation. In particular, the monthly mean temperature in the winter season affected the numbers of the Dione`s rat snake and the Korean tiger keelback snake. These results indicate that amphibian and reptile communities are responding to climate change in a variety of ways.
Discrete Curvature and Abelian Groups

Abstract We study a natural discrete Bochner-type inequality on graphs, and explore its merit as a notion of “curvature” in discrete spaces. An appealing feature of this discrete version of the so-called ${{\Gamma }_{2}}$ -calculus (of Bakry-Émery) seems to be that it is fairly straightforward to compute this notion of curvature parameter for several specific graphs of interest, particularly, abelian groups, slices of the hypercube, and the symmetric group under various sets of generators. We further develop this notion by deriving Buser-type inequalities (à la Ledoux), relating functional and isoperimetric constants associated with a graph. Our derivations provide a tight bound on the Cheeger constant (i.e., the edge-isoperimetric constant) in terms of the spectral gap, for graphs with nonnegative curvature, particularly, the class of abelian Cayley graphs, a result of independent interest.
Ultrasonic local positioning system for mobile robot navigation: From low to high level processing

This paper presents the different levels of signal processing applied to an extensive Ultrasonic Local Positioning System (ULPS) intended for mobile robot (MR) indoor navigation. The working area is covered using several single LPSs, each of them composed of a set of closely arranged ultrasonic beacons. Low-level signal processing deals with the simultaneous encoded emission of the beacons that compose each single LPS and the detection carried out in each ultrasonic receiver on board the MR, with the aim of determining Differences of Times of Flights (DoTFs) to be applied to a positioning algorithm. High-level signal processing takes into account the positions obtained with each single ULPS to reference them to a global coordinate system and to perform navigation tasks in which the typical cumulative errors of MR odometer are corrected. The whole system has been developed and tested within the LORIS project.