Miracle-dz/UniFAR-FTUs huggingface dataset:
Program comprehension as fact finding

Little is known about how developers think about design during code modification tasks or how experienced developers' design knowledge helps them work more effectively. We performed a lab study in which thirteen developers worked for 3 hours under-standing the design of a 54 KLOC open source application. Par-ticipants had from 0 to 10.5 years of industry experience and were grouped into three "experts" and ten "novices. " We observed that participants spent their time seeking, learning, critiquing, explain-ing, proposing, and implementing facts about the code such as "getFoldLevel has effects". These facts served numerous roles, such as suggesting changes, constraining changes, and predicting the amount of additional investigation necessary to make a change. Differences between experts and novices included that the experts explained the root cause of the design problem and made changes to address it, while novice changes addressed only the symptoms. Experts did not read more methods but also did not visit some methods novices wasted time understanding. Experts talked about code in terms of abstractions such as "caching" while novices more often described code statement by statement. Ex-perts were able to implement a change faster than novices. Experts perceived problems novices did not and were able to explain facts novices could not. These findings have interesting implications for future tools.
Identification of the larval and juvenile stages of the Cubera Snapper, Lutjanus cyanopterus, using DNA barcoding

The larvae and newly-settled juveniles of the Cubera Snapper, Lutjanus cyanopterus, are identified by DNA barcoding. Four larvae and three small juveniles of L. cyanopterus were detected among a large collection of pelagic larvae and a smaller collection of settled juveniles from the Caribbean coast of Panama. The mtDNA COI barcode sequences from the larvae and juveniles were virtually identical to sequences from adults sampled from the spawning aggregation in St. Thomas, USVI. Barcode sequences for the eleven regional species of Lutjanus species (sensu lato) were obtained and they exhibited deep interspecific divergences that allowed for efficient discrimination among the western Atlantic snapper species. The nearest neighbor species, the Mutton Snapper L. analis, was more than 11% divergent from L. cyanopterus. Cubera Snapper larvae are characterized by prominent melanophores along the outer spinous-dorsal-fin membranes and along the outer third of the longer pelvic-fin membranes. They are morphologically distinct from the late-stage larvae of the other regional snappers by their relatively wider caudal peduncle and their relative dorsal-spine lengths. Juveniles retain the black outer portion of the dorsal and pelvic-fin membranes and have a smaller body-depth than other regional snapper juveniles. The size at settlement is about 18 mm SL, relatively large for lutjanids. Daily otolith increments from L. cyanopterus larvae and juveniles indicate a pelagic larval duration of about 29 days with backcalculated spawning and settlement dates around the new moon. Although smaller adult Cubera Snappers can appear very similar to the Gray Snapper, L. griseus, the larvae and juveniles are quite different. In this case, the early life history stages reflect the deep genetic divergence between the two species while the adult forms converge in appearance.
Gender Difference and Spatial Heterogeneity in Local Obesity

This study asks if there is gender-specific spatial heterogeneity in local obesity. By using the 2015 Korea Community Health Survey and employing spatial analyses, this study found that there is considerable gender-specific spatial heterogeneity in local obesity rates. More specifically, we found that: (1) local obesity rates are more spatially dependent for women than for men; (2) environmental factors, in general, have stronger effects on local obesity rates for women than for men; (3) environmental factors have more spatially varying effects on local obesity rates for women than for men. Based on these findings, we suggest that policies for obesity prevention should not be based on the assumption of spatial homogeneity and gender indifference, but rather should be refined based on gender-specific spatial heterogeneity in local obesity.
Thermal noise as a spectroscopic tool to determine transport properties

The utilization of thermal fluctuations or Johnson/Nyquist noise as a spectroscopic method to determine transport properties in conductors or semiconductors is developed. The autocorrelation function is obtained from power spectral density measurements thus enabling electronic transport property calculation through the Green–Kubo formalism. This experimental approach is distinct from traditional numerical methods such as molecular dynamics simulations, which have been used to extract the autocorrelation function and directly related physics only. This work reports multi-transport property measurements consisting of the electronic relaxation time, resistivity, mobility, diffusion coefficient, electronic contribution to thermal conductivity and Lorenz number from experimental data. Double validation of the experiment was accomplished through the use of a standard reference material and a standard measurement method, i.e. four-probe collinear resistivity technique. Thermal noise measurements resulted in a 1.1 and 5% agreement with the reference material and four-probe values, respectively. Additional measurements were also taken on nanoscale Au and Cu thin films. Specifically, the validated spectroscopic methodology was applied to 30 nm Au and Cu thin films to obtain transport property data that was again compared to four-probe resistivity measurements. Comparative analysis of the resistivity data showed agreement within 13.6 and 4.8% for the Au and Cu samples, respectively, thus lending further credibility to the experimental method and theory.
A Combined Process for Production of Fumaric Acid and Xylooligosaccharides from Corncob

Production of fumaric acid and xylooligosaccharides from corncob was investigated using a combined process. Corncob was fractionated into a cellulose-rich fraction and a hemicellulose-rich fraction by an alkali pretreatment. The cellulose-rich fraction was converted into fumaric acid by Rhizopus oryzae in fed-batch simultaneous saccharification and fermentation (SSF). Maximal fumaric acid concentration reached 35.22 g/L at a final 15% (w/v) solid loading in the fed-batch SSF. The hemicellulose-rich fraction was converted into xylooligosaccharides (XOSs) by endo-β-1,4-xylanase. The yield of XOSs was 62.35% after 24 h of xylanase hydrolysis. Xylobiose, xylotriose, and xylotetraose were the three major components in the XOSs. A mass balance analysis demonstrated that 100.6 g of fumaric acid and 148.1 g of XOSs were produced from 1000 g of dry corncob matter. The production of fumaric acid and XOSs by the combined process could make the utilization of corncob more efficient and more promising.
Optimal design of non-orthogonal multiple access with wireless power transfer

We study a wireless-powered uplink communication system with non-orthogonal multiple access (NOMA), consisting of one base station and multiple energy harvesting users. We focus on data rates optimization and fairness increase. We show that the formulated optimization problems can be optimally and efficiently solved by either linear programming methods or convex optimization, which means that the proposed scheme can be easily implemented in practical applications. Simulation results illustrate that the proposed scheme outperforms the baseline orthogonal multiple access scheme, while they reveal the dependence between sum-throughput, minimum data rate, and harvested energy.
Adaptive zero padded CB-FMT for LTE uplink transmission in the high mobility scenario

LTE is the most recent standard for the mobile cellular communication. To achieve high speed communications, multi-carrier modulations have been adopted both for the downlink and the uplink. In the LTE downlink, OFDMA (the multi-user version of OFDM) has been chosen. The LTE uplink uses instead SC-FDMA modulation, an OFDM alternative. In this work, the use of CB-FMT, jointly with SC-FDMA, is analyzed in the high mobility scenario. Numerical results show that CB-FMT outperforms SC-FDMA in several cases. Thus, an adaptive implementation architecture that allows to flexibly choose the modulation scheme is proposed to maximize the achievable rate. Furthermore, for compliance with existing LTE parameters, frequency domain zero padded CB-FMT is proposed, and the problem of designing optimal capacity wise waveforms is considered.
Sequence-dependent cluster analysis of biomineralization peptides

Abstract A reliable and statistically valid classification of biomineralization peptides is herein presented. 27 biomineralization peptides (BMPep) were randomly selected as representative samples to establish the classification system using k-means method. These biomineralization peptides were either discovered through isolation from various organisms or via phage display. Our findings show that there are two types of biomineralization peptides based on their length, molecular weight, heterogeneity, and aliphatic residues. Type-1 BMPeps are more commonly found and exhibit higher values for these significant clustering variables. In contrast are the type-2 BMPeps, which have lower values for these parameters and are less common. Through our clustering analysis, a more efficient and systematic approach in BMPep selection is possible since previous methods of BMPep classification are unreliable.
Re-Emergence of Dengue Virus Type 3 in Canton, China, 2009–2010, Associated with Multiple Introductions through Different Geographical Routes

Background Endemic dengue virus type 3 (DENV-3) infections have not been reported in Canton, China, since 1980. In March 2009, DENV-3 was isolated for the second time, occurring about 30 years after the previous circulation. In August, 3 other cases emerged. One much larger outbreak occurred again in 2010. To address the origin and particularly to determine whether the outbreaks were caused by the same viral genotype, we investigated the epidemiological and molecular characteristics of the introduction, spread and genetic microevolution of DENV-3 involved. Methodology/Principal Findings Three imported cases (index-1,2,3) separately traveled back from Vietnam, India and Tanzania, resulted in 1, 3 and 60 secondary autochthonous cases, respectively. In autochthonous cases, 64.6% positive in IgM anti-DENV and 18.6% in IgG from a total of 48 submitted serum samples, accompanied by 7 DENV-3 isolates. With 99.8%, 99.7%, and 100% envelope gene nucleotidic identity, 09/GZ/1081 from index-1 and endemic strain (09/GZ/1483) belonged to genotype V; 09/GZ/10616 from index-2 and endemic strains (09/GZ/11144 and 09/GZ/11194) belonged to genotype III Clade-A; and 10/GZ/4898 from index-3 and all four 2010 endemic DENV-3 strains belonged to genotype III Clade-B, respectively. Conclusions/Significance Both epidemiological and phylogenetic analyses showed that the 2010 outbreak of dengue was not a reemergence of the 2009 strain. Introductions of different genotypes following more than one route were important contributory factors for the 2009–2010 dengue epidemics/outbreaks in Canton. These findings underscore the importance of early detection and case management of imported case in preventing large-scale dengue epidemics among indigenous peoples of Canton.
Pros and Cons of Privacy by Default: Investigating the Impact on Users and Providers of Social Network Sites

Based on actual experimental findings, we present a new line of argumentation about the chances, risks and effects of a Privacy by Default regulation for users and providers of Social Network Sites (SNS). We describe three important factors that have an impact on the utility provided by SNS and measure their change through opposing status quo. On empirical grounds, the results challenge the widely accepted assumption that restrictive default privacy settings cause overly negative consequences for providers.
Depression is more than the sum score of its parts: individual DSM symptoms have different risk factors

Background For diagnostic purposes, the nine symptoms that compose the DSM-5 criteria for major depressive disorder (MDD) are assumed to be interchangeable indicators of one underlying disorder, implying that they should all have similar risk factors. The present study investigates this hypothesis, using a population cohort that shifts from low to elevated depression levels. Method We assessed the nine DSM-5 MDD criterion symptoms (using the Patient Health Questionnaire; PHQ-9) and seven depression risk factors (personal and family MDD history, sex, childhood stress, neuroticism, work hours, and stressful life events) in a longitudinal study of medical interns prior to and throughout internship (n = 1289). We tested whether risk factors varied across symptoms, and whether a latent disease model could account for heterogeneity between symptoms. Results All MDD symptoms increased significantly during residency training. Four risk factors predicted increases in unique subsets of PHQ-9 symptoms over time (depression history, childhood stress, sex, and stressful life events), whereas neuroticism and work hours predicted increases in all symptoms, albeit to varying magnitudes. MDD family history did not predict increases in any symptom. The strong heterogeneity of associations persisted after controlling for a latent depression factor. Conclusions The influence of risk factors varies substantially across DSM depression criterion symptoms. As symptoms are etiologically heterogeneous, considering individual symptoms in addition to depression diagnosis might offer important insights obfuscated by symptom sum scores.
A charge-transfer salt composed of methyl viologen and hexacyanidoferrate(II).

The methyl viologen dication, used under the name Paraquat as an agricultural reagent, is a well-known electron-acceptor species that can participate in charge-transfer (CT) interactions. The determination of the crystal structure of this species is important for accessing the CT interaction and CT-based properties. The title hydrated salt, bis(1,1'-dimethyl-4,4'-bipyridine-1,1'-diium) hexacyanidoferrate(II) octahydrate, (C12H14N2)2[Fe(CN)6]·8H2O or (MV)2[Fe(CN)6]·8H2O [MV2+ is the 1,1'-dimethyl-4,4'-bipyridine-1,1'-diium (methyl viologen) dication], crystallizes in the space group P21/c with one MV2+ cation, half of an [Fe(CN)6]4- anion and four water molecules in the asymmetric unit. The FeII atom of the [Fe(CN)6]4- anion lies on an inversion centre and has an octahedral coordination sphere defined by six cyanide ligands. The MV2+ cation is located on a general position and adopts a noncoplanar structure, with a dihedral angle of 40.32 (7)° between the planes of the pyridine rings. In the crystal, layers of electron-donor [Fe(CN)6]4- anions and layers of electron-acceptor MV2+ cations are formed and are stacked in an alternating manner parallel to the direction of the -2a + c axis, resulting in an alternate layered structure.
Replica Symmetry Breaking in Bipartite Spin Glasses and Neural Networks

Some interesting recent advances in the theoretical understanding of neural networks have been informed by results from the physics of disordered many-body systems. Motivated by these findings, this work uses the replica technique to study the mathematically tractable bipartite Sherrington-Kirkpatrick (SK) spin-glass model, which is formally similar to a restricted Boltzmann machine (RBM) neural network. The bipartite SK model has been previously studied assuming replica symmetry; here this assumption is relaxed and a replica symmetry breaking analysis is performed. The bipartite SK model is found to have many features in common with Parisi's solution of the original, unipartite SK model, including the existence of a multitude of pure states which are related in a hierarchical, ultrametric fashion. As an application of this analysis, the optimal cost for a graph partitioning problem is shown to be simply related to the ground state energy of the bipartite SK model. As a second application, empirical investigations reveal that the Gibbs sampled outputs of an RBM trained on the MNIST data set are more ultrametrically distributed than the input data themselves.
Ultrastructural, Sensory and Functional Anatomy of the Northern Elephant Seal (Mirounga angustirostris) Facial Vibrissae

Vibrissae (whiskers) play a key role in underwater orientation in foraging phocids through vibrotactile sensation processing. Our aim was to evaluate the structure of northern elephant seal (NES) vibrissae by means of light (LM) and transmission electron microscopy (TEM), in order to elucidate their function. Vibrissal follicles were processed using standardized laboratory methods and LM/TEM techniques. Individual follicular axonal numbers were counted and axonal diameter measured and averaged. NES have mystacial, rhinal, supraorbital and labial vibrissae. The vibrissal follicles are histologically subdivided into a ring, upper and lower cavernous sinuses (LCS). Each vibrissa is innervated by the deep vibrissal nerve. The average number of axons per large mystacial vibrissa is 1804 (±123), rhinal 985 (±241), supraorbital 1,064 (±204) and 374 (±65) in labial vibrissa. The entire vibrissal system carries an estimated 148 573 axons, and mystacial vibrissae alone have 125 323 axons. Axonal conduction velocity for each vibrissal type is 55.26 m/s for labial, 56.58 m/s for rhinal and 35.88 m/s for mystacial vibrissae. TEM and LM revealed a plethora of mechanoreceptors within the vibrissal follicles: Merkel cell‐neurite complexes, lanceolate and pilo‐Ruffini end organs. A vast number of sensory axons projecting from the entire vibrissal system indicate that the vibrissal sensory area takes up a large proportion of phocids’ somatosensory cortex. In conclusion, NES has highly sensitive and finely tuned vibrotactile vibrissal sense organs.
No change in energy efficiency in lactation: Insights from a longitudinal study

Lactation is the most energy‐demanding phase of reproduction for human females, but it is still unclear how women in different environments are able to meet this additional energy demand. Previous studies have investigated whether changes in metabolism could have an energy‐sparing effect in lactation, with conflicting results. Here, we asked whether increased energy efficiency in physical activity serves as an energy‐sparing mechanism in lactation.
Structure and Properties of Cellulose Nanocomposite Films Containing Melamine Formaldehyde

The cellulose nanofibril from wood is an interesting new material constituent that can provide strong reinforcement in polymer nanocomposites due to the high stiffness of the cellulose crystals and the network formation characteristics of the nanofibrils. Cellulose nanofibrils can be used either in the form of low aspect ratio microcrystalline cellulose, MCC, or as high aspect ratio microfibrillated cellulose, MFC. The objective is to study structure-property relationships for cellulose nanofibril networks and composites. Nanocomposites based on MCC and thermoplastic polyurethane were prepared by in-situ polymerization. The cellulose nanofibrils were successfully dispersed in the matrix and the composites showed improvements in stiffness, strength, as well as in strain-to-failure. Cellulose nanofibrils reinforce the physical rubber network by strong molecular interaction with the rubber. A method that facilitates microfibrillation of the pulp cell wall during homogenization has been developed. The pulps were treated with a combination of beating and enzymatic treatment prior to homogenization. The enzymatic pretreatment was found to facilitate the microfibrillation and the mechanisms are discussed. The resulting MFC nanofibrils were of high aspect ratio. Cellulose nanofibril networks of high toughness were prepared from MFC and studied with respect to the structure and mechanical properties. These films have a porous structure and the nanofibrils are more in-plane than in-space oriented. Tensile testing showed that the strength is dependent on the average molecular weight of the cellulose. The MFC of the highest molecular weight showed a modulus of 13.2 GPa, tensile strength as high as 214 MPa and 10.1% strain-to-failure, at a porosity of 28%. Composites of high fiber content have been prepared by addition of melamine formaldehyde to MFC films. These composites show increased stiffness and strength, at the cost of strain-to-failure. Composites were also prepared by impregnating MFC nanofibril networks with a hyperbranched polymer. The matrix was crosslinked and strong interactions with the nanofibrils were formed. By DMA two Tg’s were observed for the composites with 0.26 and 0.43 volume fraction nanofibrils. The Tg of the matrix was observed as well as a Tg at higher temperatures. This corresponds to molecules with constrained mobility by increased interactions with the cellulose nanofibril surfaces.
Fine particulate matter concentrations in smoking households: just how much secondhand smoke do you breathe in if you live with a smoker who smokes indoors?

Objective Using data on fine particulate matter less than 2.5 μm (PM2.5) concentrations in smoking and non-smoking homes in Scotland to estimate the mass of PM2.5 inhaled by different age groups. Methods Data from four linked studies, with real-time measurements of PM2.5 in homes, were combined with data on typical breathing rates and time-activity patterns. Monte Carlo modelling was used to estimate daily PM2.5 intake, the percentage of total PM2.5 inhaled within the home environment and the percentage reduction in daily intake that could be achieved by switching to a smoke-free home. Results Median (IQR) PM2.5 concentrations from 93 smoking homes were 31 (10–111) μg/m3 and 3 (2–6.5) μg/m3 for the 17 non-smoking homes. Non-smokers living with smokers typically have average PM2.5 exposure levels more than three times higher than the WHO guidance for annual exposure to PM2.5 (10 μg/m3). Conclusions Fine particulate pollution in Scottish homes where smoking is permitted is approximately 10 times higher than in non-smoking homes. Taken over a lifetime many non-smokers living with a smoker inhale a similar mass of PM2.5 as a non-smoker living in a heavily polluted city such as Beijing. Most non-smokers living in smoking households would experience reductions of over 70% in their daily inhaled PM2.5 intake if their home became smoke-free. The reduction is likely to be greatest for the very young and for older members of the population because they typically spend more time at home.