Miracle-dz/UniFAR-FTUs huggingface dataset:
Using an Online Homework System Enhances Students' Learning of Physics Concepts in an Introductory Physics Course

We report the results of a comparison of student understanding of physics concepts with and without online homework, as measured by the force concept inventory. We compared students in large introductory courses taught by interactive engagement and noninteractive engagement methods and with ungraded homework and with online homework. We also compared the understanding of students in different grade subgroups. The increase in the average force concept inventory normalized gain was statistically significant for all students taught with online homework, indicating that graded homework increases student understanding of physics concepts. The gain was significantly higher for those students taught with interactive engagement methods together with online homework. The C grade subgroup taught by interactive engagement methods benefited more from the implementation of online homework than the other subgroups.
Receptor Tyrosine Kinases: Molecular Switches Regulating CNS Axon Regeneration

The poor or lack of injured adult central nervous system (CNS) axon regeneration results in devastating consequences and poor functional recovery. The interplay between the intrinsic and extrinsic factors contributes to robust inhibition of axon regeneration of injured CNS neurons. The insufficient or lack of trophic support for injured neurons is considered as one of the major obstacles contributing to their failure to survive and regrow their axons after injury. In the CNS, many of the signalling pathways associated with neuronal survival and axon regeneration are regulated by several classes of receptor tyrosine kinases (RTK) that respond to a variety of ligands. This paper highlights and summarises the most relevant recent findings pertinent to different classes of the RTK family of molecules, with a particular focus on elucidating their role in CNS axon regeneration.
Shallow Whole Genome Sequencing for the Assembly of Complete Chloroplast Genome Sequence of Arachis hypogaea L.

The chloroplast (CP) is a plant organelle originated from cyanobacteria through symbiosis and had become an important component of the plant cell. It is the reaction center for the photosynthesis and also for several steps in the biosynthetic pathways of fatty acids, vitamins, pigments and amino acids. The CP genome is highly conserved in land plants (Raubeson and Jansen, 2005). The CP genome is circular and exhibits a quadripartite genome structure consisting of a large single copy region (LSC) and a small single copy region (SSC), separated by a pair of inverted repeats (IRs) with a few exceptions where loss of an IR or the SSC was observed. The size of the CP genome varies from 19 to 217 Kb in land plants, and the IRs are usually 20–26 kb in length (http://www.ncbi.nlm.nih.gov/genome/organelle/). Lack of recombination makes the CP genome an ideal target for phylogenetic studies (Ravi et al., 2008; Wu and Ge, 2012). Arachis hypogaea L. also known as groundnut is an herbaceous plant belonging to the Fabaceae family. It has an allotetraploid genome (AABB; 2n = 4x = 40) with a size of about 2.8 Gb. There have been many speculations regarding the ancestors of A and B subgenomes of A. hypogaea and proved to have originated through a hybridization event between Arachis ipaensis L. (B subgenome) and Arachis duranensis L. (A subgenome) (Kochert et al., 1996; David et al., 2016). It is one of the major edible oilseed crops in the world, and India is the second largest producer accounting for about 15% of the world production (FAOSTAT, 2015). Kernels of A. hypogaea L. contains 43–50% oil and 23–26% proteins. The oil comprises majorly of palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), arachidic acid (20:0), eicosenoic acid (20:1), behemic acid (22:0), and lignoseric acid (24:0) along with trace amounts of palmitoleic acid (16:1). The mono and poly-unsaturated fatty acids, oleic acid and linoleic acid constitute about 75% of the total oil content (Shiv, 1982). Many attempts have successfully been made to improve the crop yield, drought resistance, disease resistance and other characteristics of A. hypogaea L. using classical breeding as well as genetic engineering using nuclear transformation. Chloroplast transformation by homologous recombination for producing transgenic plants is also possible due to the presence of candidate loci on the CP genome. Additionally, Genetic engineering of chloroplast genome when compared to nuclear transformation is environment-friendly; it minimizes the pleiotropic effects along with containment of the foreign genes (Daniell et al., 2005). Hence, the availability of the complete chloroplast genome of A. hypogaea L. will be an invaluable resource for designing and evaluating efficient chloroplast transformation experiments.
Geometric Applications of a Randomized Optimization Technique

Abstract. We propose a simple, general, randomized technique to reduce certain geometric optimization problems to their corresponding decision problems. These reductions increase the expected time complexity by only a constant factor and eliminate extra logarithmic factors in previous, often more complicated, deterministic approaches (such as parametric searching). Faster algorithms are thus obtained for a variety of problems in computational geometry: finding minimal k -point subsets, matching point sets under translation, computing rectilinear p -centers and discrete 1-centers, and solving linear programs with k violations.
Classification and diagnosis of ear malformations

In the ENT region 50% of the malformations affect the ear. Malformations of the outer and middle ear are predominantly unilateral (ca. 70-90%) and mostly involve the right ear. Inner ear malformations can be unilateral or bilateral. The incidence of ear malformations is approximately 1 in 3800 newborns. Ear malformations may be genetic (associated with syndromes or not, with family history, spontaneous mutations) or acquired in nature. Malformations can affect the outer ear (pinna and external auditory canal, EAC), middle ear and inner ear, not infrequently in combination. Formal classification is advisable in order to be able to predict the prognosis and compare treatment schedules. Various classifications have been proposed: pinna and EAC malformations according to Weerda [1], middle ear malformations according to Kösling [2], and inner ear malformations according to Jackler [3], [4], to Marangos [5] and to Sennaroglu [6]. Additionally, we describe Altmann’s classification of atresia auris congenita [7] and the Siegert-Mayer-Weerda score [8] for EAC and middle ear malformations, systems of great practicability that are in widespread clinical use. The diagnostic steps include clinical examination, audiological testing, genetic analysis and, especially, CT and MRI. These imaging methods are most usefully employed in combination. Precise description of the malformations by means of CT and MRI is indispensable for the planning and successful outcome of operative ear reconstruction and rehabilitation procedures, including cochlear implantation.
Subtropical Low Cloud Response to a Warmer Climate in a Superparameterized Climate Model. Part II: Column Modeling with a Cloud Resolving Model

A cloud resolving model (CRM) is used to investigate the low‐cloud increase due to a 2 K SST increase in the SP‐CAM superparameterized climate model. Of particular interest is the sensitivity of cloud changes to the CRM resolution (4 km horizontal, 30 vertical levels) in SP‐CAM. The CRM is run in column‐modeling framework using SP‐CAM composite cloud regimes. The experiments are run to steady state using composite advective tendencies, winds, and sea‐surface temperature from the control and +2 K climates of SP‐CAM. A new weak temperature gradient algorithm based on an idealized form of gravity wave adjustment is used to adjust vertical motion in the column to keep the simulated virtual temperature profile consistent with the corresponding SP‐CAM composite profile. Humidity is also slowly relaxed toward the SP‐CAM composite above the boundary layer. With SP‐CAM grid resolution, the CRM shows +2 K low cloud increases similar to SP‐CAM. With fine grid resolution, the CRM‐simulated low cloud fraction and its increase in a warmer climate are much smaller. Hence, the negative low cloud feedbacks in SP‐CAM may be exaggerated by under‐resolution of trade cumulus boundary layers.
Pitfalls and Caveats in BRCA Sequencing

Between 5 and 10% of breast cancer cases are considered to result from hereditary predisposition. Germ-line mutations in BRCA1 and BRCA2 are responsible for an inherited predisposition of breast and ovarian cancer. Direct nucleotide sequencing is considered the gold standard technique for mutation detection for genes such as BRCA1 and BRCA2. In many laboratories that analyze BRCA1 and BRCA2, previous to direct sequencing, screening techniques to identify sequence variants in the PCR amplicons are performed. The mutations detected in these genes may be frameshift mutations (insertions or deletions), nonsense mutations, or missense mutations. The clinical interpretation of the mutation as the cause of the disease may be difficult to establish in the case of missense mutations. Only in 30–70% of the families in which a hereditary component is suspected, a mutation in BRCA1 and/or BRCA2 is detected. Negative results may be due to: wrong selection of the proband; mutations in the regulatory portion of the genes; gene silencing due to epigenetic phenomena; or large genomic rearrangements that produce deletions of whole exons. Another possibility that explains the lack of detection of alterations in BRCA1 or BRCA2 is the presence of mutations in undiscovered genes or in genes that interact with BRCA1 and/or BRCA2, which may be low-penetrance genes, like CHEK2.
Effect of thoracentesis on respiratory mechanics and gas exchange in the patient receiving mechanical ventilation.

BACKGROUND This study reports the effect of thoracentesis on respiratory mechanics and gas exchange in patients receiving mechanical ventilation. STUDY DESIGN Prospective. SETTING University hospital. PATIENTS Eight patient receiving mechanical ventilation with unilateral (n = 7) or bilateral (n = 1) large pleural effusions. INTERVENTION Therapeutic thoracentesis (n = 9). MEASUREMENTS Resistances of the respiratory system measured with the constant inspiratory flow interrupter method measuring peak pressure and plateau pressure, effective static compliance of the respiratory system (Cst,rs), work performed by the ventilator (Wv), arterial blood gases, mixed exhaled Pco2, and pleural liquid pressure (Pliq). RESULTS Thoracentesis resulted in a significant decrease in Wv and Pliq. Thoracentesis had no significant effect on dynamic compliance of the respiratory system; Cst,rs; effective interrupter resistance of the respiratory system, or its subcomponents, ohmic resistance of the respiratory system and additional (non-ohmic) resistance of the respiratory system; or intrinsic positive end-expiratory pressure (PEEPi). Indices of gas exchange were not significantly changed by thoracentesis. CONCLUSIONS Thoracentesis in patients receiving mechanical ventilatory support results in significant reductions of Pliq and Wv. These changes were not accompanied by significant changes of resistance or compliance or by significant changes in gas exchange immediately after thoracentesis. The reduction of Wv after thoracentesis in patients receiving mechanical ventilation is not accompanied by predictable changes in inspiratory resistance and static compliance measured with routine clinical methods. The benefit of thoracentesis may be most pronounced in patients with high levels of PEEPi.
Cholesterol shuttling is important for RNA replication of coxsackievirus B3 and encephalomyocarditis virus

Picornaviruses are a family of positive‐strand RNA viruses that includes important human and animal pathogens. Upon infection, picornaviruses induce an extensive remodelling of host cell membranes into replication organelles (ROs), which is critical for replication. Membrane lipids and lipid remodelling processes are at the base of RO formation, yet their involvement remains largely obscure. Recently, phosphatidylinositol‐4‐phosphate was the first lipid discovered to be important for the replication of a number of picornaviruses. Here, we investigate the role of the lipid cholesterol in picornavirus replication. We show that two picornaviruses from distinct genera that rely on different host factors for replication, namely the enterovirus coxsackievirus B3 (CVB3) and the cardiovirus encephalomyocarditis virus (EMCV), both recruited cholesterol to their ROs. Although CVB3 and EMCV both required cholesterol for efficient genome replication, the viruses appeared to rely on different cellular cholesterol pools. Treatments that altered the distribution of endosomal cholesterol inhibited replication of both CVB3 and EMCV, showing the importance of endosomal cholesterol shuttling for the replication of these viruses. Summarizing, we here demonstrate the importance of cholesterol homeostasis for efficient replication of CVB3 and EMCV.
A Rational Expectations Model of Financial Contagion

We develop a multiple asset rational expectations model of asset prices to study the determinants of financial market contagion, and to provide an explanation for the pattern of contagion during the Asian financial crisis. Our findings show that the pattern and severity of financial contagion depends on the size of markets' sensitivities to common macroeconomic risk factors. The amount of information asymmetry within a financial market also increases its susceptibility to contagion. We focus on contagion through the cross-market hedging of macroeconomic risks. Through this channel, idiosyncratic shocks in one market are transmitted to others. Interestingly, contagion can occur between markets that have no macroeconomic risks in common. In addition, contagion occurs in the absence of any news, and before the macroeconomic risk factors are realized. Because contagion occurs through hedging, the pattern of contagion is strongly influenced by the presence or absence of derivatives markets for unbundling and hedging the macroeconomic risks. Errors in market participants' beliefs about dynamic hedging activity influence the pattern of contagion and, in some cases, strongly magnify the size of the contagious price responses.
Modulation of Human Monocyte Leukotactic Responsiveness by Thromboxane A2 and 12‐Hydroxyheptadecatrienoic Acid (12‐HHT)

The leukotactic responsiveness of human peripheral blood monocytes is regulated by the cell‐directed inhibitor of monocyte leukotaxis, CDI‐MLx. The actions of CDI‐MLx on normal monocytes in vitro were abrogated by co‐incubation with inhibitors of cyclooxygenase and thromboxane synthetase with indomethacin and dazmegrel (UK‐38,465) being most active. The actions of CDI‐MLx were mimicked by the thromboxane A2 analogue, U‐46619, and by 12‐HHT with half‐maximal inhibition observed at 10−10M; PGE2 was 1000‐fold less active. SQ 29,548, a thromboxane A2 receptor antagonist, blocked the effects of CDI‐MLx, U‐46619, and 12‐HHT. Production of PQE2 and thromboxane B2 by purified monocytes was stimulated by CDI‐MLx and this effect was also blocked by indomethacin, dazmegrel, and dazoxiben. These data suggest a major regulatory role for thromboxane synthetase products in human monocyte leukotaxis.
Peripheral blood mitochondrial DNA content in relation to circulating metabolites and inflammatory markers: A population study

Mitochondrial DNA (mtDNA) content might undergo significant changes caused by metabolic derangements, oxidative stress and inflammation that lead to development and progression of cardiovascular diseases. We, therefore, investigated in a general population the association of peripheral blood mtDNA content with circulating metabolites and inflammatory markers. We examined 310 subjects (50.6% women; mean age, 53.3 years) randomly selected from a Flemish population. Relative mtDNA content was measured by quantitative real-time PCR in peripheral blood cells. Peak circulating metabolites were quantified using nuclear magnetic resonance spectroscopy. The level of inflammation was assessed via established inflammatory markers. Using Partial Least Squares analysis, we constructed 3 latent factors from the 44 measured metabolites that explained 62.5% and 8.5% of the variance in the contributing metabolites and the mtDNA content, respectively. With adjustments applied, mtDNA content was positively associated with the first latent factor (P = 0.002). We identified 6 metabolites with a major impact on the construction of this latent factor including HDL3 apolipoproteins, tyrosine, fatty acid with αCH2, creatinine, β-glucose and valine. We summarized them into a single composite metabolite score. We observed a negative association between the composite metabolic score and mtDNA content (P = 0.001). We also found that mtDNA content was inversely associated with inflammatory markers including hs-CRP, hs-IL6, white blood cell and neutrophil counts as well as neutrophil-to-lymphocyte ratio (P≤0.0024). We demonstrated that in a general population relative peripheral blood mtDNA content was associated with circulating metabolites indicative of perturbed lipid metabolism and with inflammatory biomarkers.
Clients' Perceptions of the Therapeutic Process

Abstract Recently researchers in the family therapy field have encouraged a focus on aspects of therapy common across all models that are important to therapeutic change. The purpose of this study was to build on the “common factors” literature by exploring clients' perspectives of what was useful to their therapeutic experience. Quantitative and qualitative measures were used to collect data from 41 clients who participated in therapy at a university-based family therapy clinic. Quantitative results indicated that therapeutic relationship, client motivation, extratherapeutic factors, and hope and expectancy accounted for 49% of the variance of clients' perception of change and 73% of the variance of clients' perceptions of therapy helpfulness. Qualitative results indicated the therapeutic relationship to be the most helpful aspect of clients' therapeutic experience.
CRUDAW: A Novel Fuzzy Technique for Clustering Records Following User Defined Attribute Weights

We present a novel fuzzy clustering technique called CRUDAW that allows a data miner to assign weights on the attributes of a data set based on their importance (to the data miner) for clustering. The technique uses a novel approach to select initial seeds deterministically (not randomly) using the density of the records of a data set. CRUDAW also selects the initial fuzzy membership degrees deterministically. Moreover, it uses a novel approach for measuring distance considering the user defined weights of the attributes. While measuring the distance between the values of a categorical attribute the technique takes the similarity of the values into consideration instead of considering the distance to be either 0 or 1. Complete algorithm for CRUDAW is presented in the paper. We experimentally compare our technique with a few existing techniques -- namely SABC, GFCM, and KL-FCM-GM based on various evaluation criteria called Silhouette coefficient, F-measure, purity and entropy. We also use t-test, confidence interval test and time complexity in evaluating the performance of our technique. Four data sets available from UCI machine learning repository are used in the experiments. Our experimental results indicate that CRUDAW performs significantly better than the existing techniques in producing high quality clusters.
Wave-Driven Mean Tropical Upwelling in the Lower Stratosphere

The mean meridional circulation induced by zonal momentum forcing is considered in the context of (i) a wave‐mean model, in which the momentum forcing arises naturally from the explicit representation of the stratospheric wave response to lower boundary forcing, and (ii) a zonally symmetric model, in which the momentum forcing is prescribed externally. Wave forcing is confined to one hemisphere, as a simple representation of the difference between the Northern and Southern Hemispheres. The main focus of the paper is on how the upwelling branch of the circulation in the Tropics depends on nonlinearity, model diffusion, and the transient effects of the seasonal cycle. Significant tropical upwelling can occur in the steady state if the zonal momentum force extends into the subtropics, provided the forcing is strong enough to redistribute angular momentum throughout the Tropics. The circulation in these strongly forced cases depends nonlinearly on the forcing amplitude. If the forcing is weak, so that the dynamics are approximately linear, significant tropical upwelling can occur in the steady state if (i) the radiative equilibrium temperature is such that angular momentum contours tilt poleward and upward, as at the winter solstice, or (ii) the model diffusion is large. In seasonally varying cases, weak subtropical forcing can also induce a time average tropical upwelling through the interaction of the transient angular momentum distribution and the transient forcing. When the forcing is strong, the effect of the seasonal cycle leads to an increase in the tropical upwelling beyond that of the steady-state response.
Seasonal Patterns of Body Condition, Hydration State, and Activity of Gila Monsters (Heloderma suspectum) at a Sonoran Desert Site

Abstract Animals in nature use synergistic behavioral and physiological responses to cope with variation in resource availability. We used a combination of traditional tools (i.e., radiotelemetry, body-condition measurements, plasma osmometry, and direct observation) and contemporary techniques (i.e., implanted temperature loggers and portable ultrasonography) to identify seasonal patterns of body condition, hydration state, and surface activity of 16 free-living Gila Monsters during two active seasons. Despite seasonal drought each year, Gila Monster snout–vent length increased during the study; yet body mass, tail volume, and hydration state decreased. Generally, surface activity was associated with rainy periods, and males were significantly more active than females but only during the reproductive season. Our results indicate that Gila Monsters combine flexible behavioral patterns (i.e., the timing and duration of surface activity), resource storage and economical use, and tolerance of substantial physiological disturbance to endure seasonal resource limitations at a site in the Arizona-Upland subdivision of the Sonoran Desert.