Miracle-dz/UniFAR-FTUs huggingface dataset:
Sub‐threshold transcranial magnetic stimulation applied after the go‐signal facilitates reaction time under control but not startle conditions

The presentation of a startling acoustic stimulus (SAS) in a simple reaction time (RT) task significantly reduces RT due to the involuntary early initiation of a prepared movement; however, the underlying neural mechanism remains unclear. It has been proposed that a SAS triggers a cortically stored motor program by involuntarily increasing initiation‐related activation. Sub‐threshold transcranial magnetic stimulation (TMS) can be used to investigate cortical processes, as it increases cortical excitability for 6–30 ms and significantly reduces RT. The purpose of the present experiments was to determine whether the application of sub‐threshold TMS over motor cortex in close temporal proximity to a SAS would facilitate startle RT in the same manner as control RT, providing evidence for cortical involvement in startle‐related RTs. Participants completed a simple RT task requiring targeted wrist extension in response to an auditory go‐signal, which was randomly replaced by a SAS on 25% of trials. On a subset of trials, sub‐threshold TMS was applied 30 ms following the go‐signal in control trials or at −15, 0, +15 or +30 ms with respect to the SAS in startle trials. In all three experiments, sham and real TMS significantly reduced RT in control trials, with real TMS having a larger effect, but there was no effect of either real or sham TMS on startle‐related RT. These results suggest that there may be limited cortical involvement in the initiation of movements in response to a SAS. As an alternative, startle may produce the fastest possible RTs, with little room for additional facilitation.
Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants. Antimicrobial resistance was clearly species-dependent. Resistance to quinupristin/dalfopristin was common in Staphylococcus gallinarum (prevalence of 98%), whereas S. cohnii and S. arlettae were frequently resistant to erythromycin (prevalence of 63 and 100%, respectively). Prevalence of resistance was 10% against β-lactams and tetracyclines. In contrast, resistance to antimicrobials critically important for human medicine, namely vancomycin, fluoroquinolones, linezolid and daptomycin, was uncommon (< 1%). Genes encoding multidrug-resistance efflux pumps and resistance-associated residues in deducted amino acid sequences of the folP gene were the most frequent mechanisms of resistance, regardless of species. The estimated prevalence of the mecA gene was 17% for S. epidermidis. Several genes, including blaZ, mecA, fexA, erm, mphC, msrA, and tet were associated with drug-specific resistance, whereas other elements were not. There were specific residues in gyrB for all isolates of species intrinsically resistant to novobiocin. This study provided consensus protein sequences of key elements previously associated with resistance for 25 species of non-aureus staphylococci from dairy cattle. These results will be important for evaluating effects of interventions in antimicrobial use in Canadian dairy herds.
The empirical relationship between satellite-derived tropospheric NO 2 and fire radiative power and possible implications for fire emission rates of NO x

Abstract. Nitrogen oxides (NOx) play key roles in atmospheric chemistry, air pollution, and climate. While the largest fraction of these reactive gases is released by anthropogenic emission sources, a significant amount can be attributed to vegetation fires. In this study, NO2 from GOME-2 on board EUMETSAT's MetOp-A and OMI on board NASA's Aura as well as fire radiative power (FRP) from the measurements of MODIS on board NASA's Terra and Aqua satellites are used to derive fire emission rates (FERs) of NOx for different types of vegetation using a simple statistical approach. Monthly means of tropospheric NO2 vertical columns (TVC NO2) have been analyzed for their temporal correlation with the monthly means of FRP for five consecutive years from 2007 to 2011 on a horizontal 1° × 1° grid. The strongest correlation is found to be largely confined to tropical and subtropical regions, which account for more than 80% of yearly burned area, on average, globally. In these regions, the seasonal variation of fire intensity, expressed by the FRP data, is similar to the pattern of TVC NO2. As chemical models typically require values for the amount of NOx being released as a function of time, we have converted the retrieved TVC NO2 into production rates of NOx from fire (Pf) by assuming a constant lifetime of NOx. The comparison between Pf and NOx emissions from the Global Fire Emissions Database (GFEDv3.1) over 5 characteristic biomass burning regions in the tropics and subtropics shows good agreement. By separating the monthly means of Pf and FRP according to land cover type, FERs of NOx could be derived for different biomes. The estimated FERs for the dominating types of vegetation burned are lowest for open shrublands and savannas (0.28–1.03 g NOx s−1 MW−1) and highest for croplands and woody savannas (0.82–1.56 g NOx s−1 MW−1). This analysis demonstrates that the strong empirical relationship between TVC NO2 and FRP and the following simplified assumptions are a useful tool for the characterization of NOx emission rates from vegetation fires in the tropics and subtropics. Possible factors affecting the magnitude of the obtained values are discussed.
Feasibility of Leveraging Crowd Sourcing for the Creation of a Large Scale Annotated Resource for Hindi English Code Switched Data: A Pilot Annotation

Linguistic code switching (LCS) occurs when speakers mix multiple languages in the same speech utterance. We find LCS pervasively in bilingual communities. LCS poses a serious challenge to Natural Language and Speech Processing. With the ubiquity of informal genres online, LCS is emerging as a very widespread phenomenon. This paper presents a first attempt at collecting and annotating a large repository of LCS data. We target Hindi English (Hinglish) LCS. We investigate the feasibility of leveraging crowd sourcing as a means for annotating the data on the word level. This paper briefly explains the setup of the experiment and data collection. It also presents statistics representing agreements among annotators over different possible categories of Hinglish words and analyzes the confidence with which a code switched word can be annotated in the correct category by humans.
Victor Almon McKusick (21 October 1921–22 July 2008): Philosophical approach and historiography

While many authors have surveyed the contributions of Victor Almon McKusick, MD (21 October 1921–22 July 2008) to establishing the field of medical genetics, no authors have reviewed his significant contributions as an historian to the field of the history of medicine. In discussing relevant biographical themes and their functional influence in his life, his philosophical approach to the study of the history of medicine and his unique historiography, blending various major schools of thought into a hybrid analytical approach to historical research, was evaluated. The evaluation drew on a series of interviews conducted with McKusick in 2004 and 2005, review of a selection of his published historical contributions, and review of secondary sources.
Structural basis for non-genuine phenolic acceptor substrate specificity of Streptomyces roseochromogenes prenyltransferase CloQ from the ABBA/PT-barrel superfamily

Acceptor substrate specificity of Streptomyces roseochromogenes prenyltransferase SrCloQ was investigated using different non-genuine phenolic compounds. RP-UHPLC-UV-MSn was used for the tentative annotation and quantification of the prenylated products. Flavonoids, isoflavonoids and stilbenoids with different types of substitution were prenylated by SrCloQ, although with less efficiency than the genuine substrate 4-hydroxyphenylpyruvate. The isoflavan equol, followed by the flavone 7,4’-dihydroxyflavone, were the best non-genuine acceptor substrates. B-ring C-prenylation was in general preferred over A-ring C-prenylation (ratio 5:1). Docking studies of non-genuine acceptor substrates with the B-ring oriented towards the donor substrate dimethylallyl pyrophosphate, showed that the carbonyl group of the C-ring was able to make stabilizing interactions with the residue Arg160, which might determine the preference observed for B-ring prenylation. No reaction products were formed when the acceptor substrate had no phenolic hydroxyl groups. This preference can be explained by the essential hydrogen bond needed between a phenolic hydroxyl group and the residue Glu281. Acceptor substrates with an additional hydroxyl group at the C3’ position (B-ring), were mainly O3’-prenylated (> 80% of the reaction products). This can be explained by the proximity of the C3’ hydroxyl group to the donor substrate at the catalytic site. Flavones were preferred over isoflavones by SrCloQ. Docking studies suggested that the orientation of the B-ring and of the phenolic hydroxyl group at position C7 (A-ring) of flavones towards the residue Tyr233 plays an important role in this observed preference. Finally, the insights obtained on acceptor substrate specificity and regioselectivity for SrCloQ were extended to other prenyltransferases from the CloQ/NhpB family.
An extension of ISO-Space for annotating object direction

In this paper, we extend an existing annotation scheme ISO-Space for annotating necessary spatial information for the task placing an specified object at a specified location with a specified direction according to a natural language instruction. We call such task the spatial placement problem. Our extension particularly focuses on describing the object direction, when the object is placed on the 2D plane. We conducted an annotation experiment in which a corpus of 20 situated dialogues were annotated. The annotation result showed the number of newly introduced tags by our proposal is not negligible. We also implemented an analyser that automatically assigns the proposed tags to the corpus and evaluated its performance. The result showed that the performance for entity tag was quite high ranging from 0.68 to 0.99 in F-measure, but not the case for relation tags, i.e. less than 0.4 in F-measure.
Real-time physical model of an Aeolian harp

A real-time physical sound synthesis model of an Aeolian harp is presented. The model uses semiempirical fluid dynamics equations to inform its operation, providing suitable parameters for users to interact. A basic wind model is included as well as an interface allowing user adjustable parameters. Sounds generated by the model were subject to objective measurements against real-world recordings, which showed that many of the physical properties of the harp were replicated in our model, but a possible link between harmonics and vibration amplitude was not. A perceptual test was performed, where participants were asked to rate sounds in terms of how plausible they were in comparison with spectral modelling synthesis and recorded Aeolian Harp samples. Evaluation showed that our model performed as well as an alternative non-physical synthesis method, but was not as authentic as actual recorded samples.
Networking for conservation: social capital and perceptions of organizational success among land trust boards

As an important component in collaborative natural resource management and nonprofit governance, social capital is expected to be related to variations in the performance of land trusts. Land trusts are charitable organizations that work to conserve private land locally, regionally, or nationally. The purpose of this paper is to identify the level of structural and cognitive social capital among local land trusts, and how these two types of social capital relate to the perceived success of land trusts. The analysis integrates data for land trusts operating in the U.S. south-central Appalachian region, which includes western North Carolina, southwest Virginia, and east Tennessee. We use factor analysis to elicit different dimensions of cognitive social capital, including cooperation among board members, shared values, common norms, and communication effectiveness. Measures of structural social capital include the size and diversity of organizational networks of both land trusts and their board members. Finally, a hierarchical linear regression model is employed to estimate how cognitive and structural social capital measures, along with other organizational and individual-level attributes, relate to perceptions of land trust success, defined here as achievement of the land trusts’ mission, conservation, and financial goals. Results show that the diversity of organizational partnerships, cooperation, and shared values among land trust board members are associated with higher levels of perceived success. Organizational capacity, land trust accreditation, volunteerism, and financial support are also important factors influencing perceptions of success among local, nonprofit land trusts.
FlattGen: Teaching tool for surface flattening

In many cases in the industry, we can face a problem, where an object has to be manufactured out of thin plane material. This is especially the case in the car, airplane, shipbuilding, textile, and shoe making industry. In order to manufacture such an object, a pattern has to be generated first. It has to be cut out from plane material and then bend to the final shape. The same problem can be found also in computer graphics, where flat patterns are used to decrease distortions in texture mapping. Therefore, it is important for designers and computer engineers to master the flat pattern generation. In literature, a great number of methods for pattern generation can be found and it is important to know their advantages and weaknesses. In this article, the application FlattGen is presented where the most important flattening methods can be seen and compared to each other. In this way, students can experiment and prepare themselves better for the future work. © 2006 Wiley Periodicals, Inc. Comput Appl Eng Educ 14: 106–119, 2006; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20060
Nutritional requirements of Streptococcus mutans.

Ten strains of Streptococcus mutans, representing four serological groups, have been grown in chemically defined media. For anaerobic growth, one of the strains required the following organic compounds: glucose, cysteine (or thioglycolic acid), biotin, p-aminobenzoic acid, thiamine, riboflavin, pyridoxine, pantothenic acid and nicotinic acid. Except for this vitamin requirement, the organism could use ammonia as the sole source of nitrogen for growth. In aerobic culture, uracil and one of the amino acids, glutamine, glutamic acid, asparagine or aspartic acid, had to be included in the medium for growth of the organism.
A composite mouse model of aplastic anemia complicated with iron overload

Iron overload is commonly encountered during the course of aplastic anemia (AA), but no composite animal model has been developed yet, which hinders drug research. In the present study, the optimal dosage and duration of intraperitoneal iron dextran injection for the development of an iron overload model in mice were explored. A composite model of AA was successfully established on the principle of immune-mediated bone marrow failure. Liver volume, peripheral hemogram, bone marrow pathology, serum iron, serum ferritin, pathological iron deposition in multiple organs (liver, bone marrow, spleen), liver hepcidin, and bone morphogenetic protein 6 (BMP6), SMAD family member 4 (SMAD4) and transferrin receptor 2 (TfR2) mRNA expression levels were compared among the normal control, AA, iron overload and composite model groups to validate the composite model, and explore the pathogenesis and features of iron overload in this model. The results indicated marked increases in iron deposits, with significantly increased liver/body weight ratios as well as serum iron and ferritin in the iron overload and composite model groups as compared with the normal control and AA groups (P<0.05). There were marked abnormalities in iron regulation gene expression between the AA and composite model groups, as seen by the significant decrease of hepcidin expression in the liver (P<0.01) that paralleled the changes in BMP6, SMAD4, and TfR2. In summary, a composite mouse model with iron overload and AA was successfully established, and AA was indicated to possibly have a critical role in abnormal iron metabolism, which promoted the development of iron deposits.
List Heaps

This paper presents a simple extension of the binary heap, the List Heap. We use List Heaps to demonstrate the idea of adaptive heaps: heaps whose performance is a function of both the size of the problem instance and the disorder of the problem instance. We focus on the presortedness of the input sequence as a measure of disorder for the problem instance. A number of practical applications that rely on heaps deal with input that is not random. Even random input contains presorted subsequences. Devising heaps that exploit this structure may provide a means for improving practical performance. We present some basic empirical tests to support this claim. Additionally, adaptive heaps may provide an interesting direction for theoretical investigation.
Efficient coding of computer generated images with acceptable picture quality

Coding of computer generated (CG) images with visually acceptable quality is studied based on the lossless/near-lossless coding methods defined in the JPEG-LS standard, including their modification. First, a color transform into YCbCr is done and its lossless coding is found to reduce the lossless coding in RGB space by 20-53%. As the normal JPEG-LS near-lossless coding methods are found not to provide acceptable image quality, another compatible method to JPEG-LS is proposed and found to reduce the bit-rate of lossless coding by about 20-30%, while keeping almost acceptable picture quality. Finally, we propose a new method that can achieve a reduction of bit-rate from YCbCr lossless coding by 22-44%, keeping acceptable image quality for both. natural and CG images, though not compatible to JPEG-LS.
Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment

Recently, it has been demonstrated that calling of copy number alterations (CNAs) from amplicon sequencing (AS) data is feasible. Most approaches, however, require non-tumor (germline) DNA for data normalization. Here, we present the method Ioncopy for CNA detection which requires no normal controls and includes a significance assessment for each detected alteration. Ioncopy was evaluated in a cohort of 184 clinically annotated breast carcinomas. A total number of 252 amplifications were detected, of which 183 (72.6%) could be validated by a call of an additional amplicon interrogating the same gene. Moreover, a total number of 33 deletions were found, whereof 27 (81.8%) could be validated. Analyzing the 16 most frequently amplified genes, validation rates of over 89% could be achieved for 11 of these genes. 11 of the top 16 genes showed significant overexpression in the amplified tumors. 89.5% of the HER2-amplified tumors were GRB7 and STARD3 co-amplified, whereas 68.4% of the HER2-amplified tumors had additional MED1 amplifications. Correlations between CNAs measured by amplicons in HER2 exons 19, 20 and 21 were strong (all R > 0.93). AS based detection of HER2 amplifications had a sensitivity of 90.0% and a specificity of 98.8% compared to the gold standard of HER2 immunohistochemistry combined with in situ hybridization. In summary, we developed and validated a novel method for detection and significance assessment of CNAs in amplicon sequencing data. Using Ioncopy, AS offers a straightforward and efficient approach to simultaneously analyze gene amplifications and gene deletions together with simple somatic mutations in a single assay.
Toward the analysis of mitochondria isolated from leukemic cells with electrochemically instrumented microwell arrays

This work deals with the development of electrochemical transducers for the analysis of the metabolic status of mitochondria isolated from leukemic cells. It proposes the use of ring nanoelectrodes (RNE) integrated into microwell arrays for the simultaneous monitoring of the oxygen (O2) consumption and the hydrogen peroxide (H2O2) production. The sensor enabled the real-time recording of the oxygen consumption of approximately 10,000 isolated mitochondria. Solutions are now proposed to detect H2O2 production and to reduce the number of mitochondria under test, targeting the single mitochondrion analysis.
Constraining the strength of the terrestrial CO 2 fertilization effectin the Canadian Earth system model version 4.2 (CanESM4.2)

Abstract. Earth system models (ESMs) explicitly simulate the interactions between the physical climate system components and biogeochemical cycles. Physical and biogeochemical aspects of ESMs are routinely compared against their observation-based counterparts to assess model performance and to evaluate how this performance is affected by ongoing model development. Here, we assess the performance of version 4.2 of the Canadian Earth system model against four land carbon-cycle-focused, observation-based determinants of the global carbon cycle and the historical global carbon budget over the 1850–2005 period. Our objective is to constrain the strength of the terrestrial CO2 fertilization effect, which is known to be the most uncertain of all carbon-cycle feedbacks. The observation-based determinants include (1) globally averaged atmospheric CO2 concentration, (2) cumulative atmosphere–land CO2 flux, (3) atmosphere–land CO2 flux for the decades of 1960s, 1970s, 1980s, 1990s, and 2000s, and (4) the amplitude of the globally averaged annual CO2 cycle and its increase over the 1980 to 2005 period. The optimal simulation that satisfies constraints imposed by the first three determinants yields a net primary productivity (NPP) increase from ∼ 58 Pg C year−1 in 1850 to about ∼ 74 Pg C year−1 in 2005; an increase of ∼ 27 % over the 1850–2005 period. The simulated loss in the global soil carbon amount due to anthropogenic land use change (LUC) over the historical period is also broadly consistent with empirical estimates. Yet, it remains possible that these determinants of the global carbon cycle are insufficient to adequately constrain the historical carbon budget, and consequently the strength of terrestrial CO2 fertilization effect as it is represented in the model, given the large uncertainty associated with LUC emissions over the historical period.