Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear Mixed Model Robust Regression

Mixed models are powerful tools for the analysis of clustered data and many extensions of the classical linear mixed model with normally distributed response have been established. As with all parametric models, correctness of the assumed model is critical for the validity of the ensuing inference. An incorrectly specified parametric means model may be improved by using a local, or nonparametric, model. Two local models are proposed by a pointwise weighting of the marginal and conditional variance-covariance matrices. However, nonparametric models tend to fit to irregularities in the data and provide fits with high variance. Model robust regression techniques estimate mean response as a convex combination of a parametric and a nonparametric model fits to the data. It is a semiparametric method by which incomplete or incorrect specified parametric models can be improved through adding an appropriate amount of the nonparametric fit. We compare the approximate integrated mean square error of the parametric, nonparametric, and mixed model robust methods via a simulation study, and apply these methods to monthly wind speed data from counties in Ireland.
Embodied Comparison of Functional Relations

The current study extends previous work of our group which aims to show that the comparison of functional relations is carried out by running dual perceptual-motor simulations. To this end, we present an experiment which tests the hypothesis that the asymmetries of human bodies may constrain performance in a relation comparison task. Participants were asked to compare functional relations between graspable objects while bearing sports weights on their wrists. The results of the experiment support the hypothesis. The fact that a manipulation of the participants’ bodies may affect performance in a purely conceptual task is pointed out as strong evidence in support of the embodied cognition approach.
No Functional Magnetic Resonance Imaging Evidence for Brightness and Color Filling-In In Early Human Visual Cortex

The brightness and color of a surface depends on its contrast with nearby surfaces. For example, a gray surface can appear very light when surrounded by a black surface or dark when surrounded by a white surface. Some theories suggest that perceived surface brightness and color is represented explicitly by neural signals in cortical visual field maps; these neural signals are not initiated by the stimulus itself but rather by the contrast signals at the borders. Here, we use functional magnetic resonance imaging (fMRI) to search for such neural “filling-in” signals. Although we find the usual strong relationship between local contrast and fMRI response, when perceived brightness or color changes are induced by modulating a surrounding field, rather than the surface itself, we find there is no corresponding local modulation in primary visual cortex or other nearby retinotopic maps. Moreover, when we model the obtained fMRI responses, we find strong evidence for contributions of both local and long-range edge responses. We argue that such extended edge responses may be caused by neurons previously identified in neurophysiological studies as being brightness responsive, a characterization that may therefore need to be revised. We conclude that the visual field maps of human V1 and V2 do not contain filled-in, topographical representations of surface brightness and color.
Structural characterization of graphene layers in various Indian coals by X-Ray Diffraction technique

The results of the structural investigation of three Indian coals showed that, the structural parameters like fa & Lc increased where as interlayer spacing d002 decreased with increase in carbon content, aromaticity and coal rank. These structural parameters change just opposite with increase in volatile matter content. Considering the 'turbostratic' structure for coals, the minimum separation between aromatic lamellae was found to vary between 3.34 to 3.61 A° for these coals. As the aromaticity increased, the interlayer spacing decreased an indication of more graphitization of the sample. Volatile matter and carbon content had a strong influence on the aromaticity, interlayer spacing and stacking height on the sample. The average number of carbon atoms per aromatic lamellae and number of layers in the lamellae was found to be 16-21 and 7-8 for all the samples.
Exclusive Breast Feeding Practice in Gangawatakoralaya MOH area, Sri Lanka

Breastfeeding is an unequalled way of providing optimal and complete nutrition for the healthy growth and development of infants. Even though the Sri Lankan mothers increasingly choosing to breastfeed their babies', the rates of exclusive breast feeding for first six months still remain low. The purpose of this study was to determine the prevalence of exclusive breastfeeding practice in Gangawatakoralaya MOH area in Sri Lanka. The study variables were the mother's occupation, level of education, parity and the sex of the baby. The statistical significance of the study variables were tested by chi-square test using SAS 9.1 and significant effects were tested using Fisher's Exact Test. An effect was considered statistically significant if p< 0.05. Out of the 350 subjects, 215 (61.43 %) mothers exclusively breast fed their children for first six months. Beside breast feeding 77 (22.0%) mothers were given water to their children during the first six months. Statistically significant number of housemaid mothers was exclusively breast fed their children compared to working mothers. Health care workers have a greater responsibility in promoting exclusive breast feeding practice thorough effective health education strategies in Sri Lanka.
Functional Classification of Genome-Scale Metabolic Networks

We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. In the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. Both strategies allow for a quantification of functional properties of metabolic networks, allowing to identify groups of organisms with similar functions. We investigate whether the functional description reflects the typical environments of the corresponding organisms by dividing all species into disjoint groups based on whether they are aerotolerant and/or photosynthetic. Despite differences in the underlying concepts, both measures display some common features. Closely related organisms often display a similar functional behavior and in both cases the functional measures appear to correlate with the considered classes of environments. Carbon utilization spectra and nutrient profiles are complementary approaches toward a functional classification of organism-wide metabolic networks. Both approaches contain different information and thus yield different clusterings, which are both different from the classical taxonomy of organisms. Our results indicate that a sophisticated combination of our approaches will allow for a quantitative description reflecting the lifestyles of organisms.
Conscience Accounting: Emotion Dynamics and Social Behavior

This paper presents theory and experiments where people's prosocial attitudes fluctuate over time following the violation of an internalized norm. We report the results of two experiments in which people who first made an immoral choice were then more likely to donate to charity than those who did not. In addition, those who knew that a donation opportunity would follow the potentially immoral choice behaved more unethically than those who did not know. We interpret this increase in charitable behavior as being driven by a temporal increase in guilt induced by past immoral actions. We term such behavior conscience accounting and discuss its importance in charitable giving and in the identification of social norms in choice behavior through time inconsistency. Data, as supplemental material, are available at http://dx.doi. org/10.1287/mnsc.2014. 1942 . This paper was accepted by Teck-Hua Ho, behavioral economics.
Antigenic and sequence analysis of H3 influenza virus haemagglutinins from pigs in Italy.

To investigate the possible mechanism of maintenance of old human influenza A (H3N2) viruses in pigs, the haemagglutinins (HAs) of seven isolates from swine were studied by analysis of nucleotide and deduced primary amino acid sequences, as well as reactivity of the HA molecule to chicken antisera and monoclonal antibodies. The swine HAs were closely similar to the HA of the A/Victoria/3/75 human variant as regards antigenic and molecular characteristics. These findings are consistent with the hypothesis that the swine HA genes were transmitted from an early human H3 virus to pigs, where they survived with limited mutations over a period of 5 years. The sequence data were also compared with swine H3 sequences to investigate genetic relationships between the H3 genes from swine viruses isolated in different geographical areas. An evolutionary tree, constructed from the nucleotide sequences of viruses isolated from pigs in China and in Italy, illustrated that, depending on the country of their isolation, the HA genes of swine influenza A (H3N2) viruses have different origins, e.g. human and avian, and evolved independently in different lineages. The study provides direct support for the hypothesis that pigs might serve as a 'mixing vessel' for the generation of pandemic strains of human influenza viruses.
New schedulability analysis for MrsP

In this paper we consider a spin-based multi-processor locking protocol, named the Multiprocessor resource sharing Protocol (MrsP). MrsP adopts a helping-mechanism where the preempted resource holder can migrate. The original schedulability analysis of MrsP carries considerable pessimism as it has been developed assuming limited knowledge of the resource usage for each remote task. In this paper new MrsP schedulability analysis is developed that takes into account such knowledge to provide a less pessimistic analysis than that of the original analysis. Our experiments show that, theoretically, the new analysis offers better (at least identical) schedulability than the FIFO non-preemptive protocol, and can outperform FIFO preemptive spin locks under systems with either intensive resource contention or long critical sections. The paper also develops analysis to include the overhead of MrsP's helping mechanism. Although MrsP's helping mechanism theoretically increases schedulability, our evaluation shows that this increase may be negated when the overheads of migrations are taken into account. To mitigate this, we have modified the MrsP protocol to introduce a short non-preemptive section following migration. Our experiments demonstrate that with migration cost, MrsP may not be favourable for short critical sections but provides a better schedulability than other FIFO spin-based protocols when long critical sections are applied.
One- vs. Three-Fraction Pancreatic Stereotactic Body Radiation Therapy for Pancreatic Carcinoma: Single Institution Retrospective Review

Background/introduction Early reports of stereotactic body radiation therapy (SBRT) for pancreatic ductal adenocarcinoma (PDAC) used single fraction, but eventually shifted to multifraction regimens. We conducted a single institution review of our patients treated with single- or multifraction SBRT to determine whether any outcome differences existed. Methods and materials Patients treated with SBRT in any setting for PDAC at our facility were included, from 2004 to 2014. Overall survival (OS), local control (LC), regional control (RC), distant metastasis (DM), and late grade 3 or greater radiation toxicities from the time of SBRT were calculated using Kaplan–Meier estimation to either the date of last follow-up/death or local/regional/distant failure. Results We identified 289 patients (291 lesions) with pathologically confirmed PDAC. Median age was 69 (range, 33–90) years. Median gross tumor volume was 12.3 (8.6–21.3) cm3 and planning target volume 17.9 (12–27) cm3. Single fraction was used in 90 (30.9%) and multifraction in 201 (69.1%) lesions. At a median follow-up of 17.3 months (IQR 10.1–29.3 months), the median survival for the entire cohort 17.8 months with a 2-year OS of 35.3%. Univariate analysis showed multifraction schemes to have a higher 2-year OS 30.5% vs. 37.5% (p = 0.019), it did not hold significance on MVA. Multifractionation schemes were found to have a higher LC on MVA (HR = 0.53, 95% CI, 0.33–0.85, p = 0.009). At 2 years, late grade 3+ toxicity was 2.5%. Post-SBRT CA19-9 was found on MVA to be a prognostic factor for OS (HR = 1.01, 95% CI, 1.01–1.01, p = 0.009), RC (HR = 1.01, 95% CI 1.01–1.01, p = 0.02), and DM (HR = 1.01, 95% CI, 1.01–1.01, p = 0.001). Conclusion Our single institution retrospective review is the largest to date comparing single and multifraction SBRT and the first to show multifraction regimen SBRT to have a higher LC than single fractionation. Additionally, we show low rates of severe late toxicity with SBRT.
How to guarantee optimal stability for most representative structures in the protein data bank

We proposed recently an optimization method to derive energy parameters for simplified models of protein folding. The method is based on the maximization of the thermodynamic average of the overlap between protein native structures and a Boltzmann ensemble of alternative structures. Such a condition enforces protein models whose ground states are most similar to the corresponding native states. We present here an extensive testing of the method for a simple residue‐residue contact energy function and for alternative structures generated by threading. The optimized energy function guarantees high stability and a well‐correlated energy landscape to most representative structures in the PDB database. Failures in the recognition of the native structure can be attributed to the neglect of interactions between different chains in oligomeric proteins or with cofactors. When these are taken into account, only very few X‐ray structures are not recognized. Most of them are short inhibitors or fragments and one is a structure that presents serious inconsistencies. Finally, we discuss the reasons that make NMR structures more difficult to recognize. Proteins 2001;44:79–96. © 2001 Wiley‐Liss, Inc.
Sexual activity increases the number of newborn cells in the accessory olfactory bulb of male rats

In rodents, sexual behavior depends on the adequate detection of sexually relevant stimuli. The olfactory bulb (OB) is a region of the adult mammalian brain undergoing constant cell renewal by continuous integration of new granular and periglomerular neurons in the accessory (AOB) and main (MOB) olfactory bulbs. The proliferation, migration, survival, maturation, and integration of these new cells to the OB depend on the stimulus that the subjects received. We have previously shown that 15 days after females control (paced) the sexual interaction an increase in the number of cells is observed in the AOB. No changes are observed in the number of cells when females are not allowed to control the sexual interaction. In the present study we investigated if in male rats sexual behavior increases the number of new cells in the OB. Male rats were divided in five groups: (1) males that did not receive any sexual stimulation, (2) males that were exposed to female odors, (3) males that mated for 1 h and could not pace their sexual interaction, (4) males that paced their sexual interaction and ejaculated one time and (5) males that paced their sexual interaction and ejaculated three times. All males received three injections of the DNA synthesis marker bromodeoxyuridine at 1h intervals, starting 1 h before the beginning of the behavioral test. Fifteen days later, males were sacrificed and the brains were processed to identify new cells and to evaluate if they differentiated into neurons. The number of newborn cells increased in the granular cell layer (GrCL; also known as the internal cell layer) of the AOB in males that ejaculated one or three times controlling (paced) the rate of the sexual interaction. Some of these new cells were identified as neurons. In contrast, no significant differences were found in the mitral cell layer (also known as the external cell layer) and glomerular cell layer (GlCL) of the AOB. In addition, no significant differences were found between groups in the MOB in any of the layers analyzed. Our results indicate that sexual behavior in male rats increases neurogenesis in the GrCL of the AOB when they control the rate of the sexual interaction.
The Association Between Blood Coagulation Activity and Lung Function: A Population-Based Study

Background Increased in susceptibility to thrombotic disease may be associated with lower lung function. If causal, this association may suggest an area for development of new interventions for lung disease. The aim of this study was to investigate the association between blood coagulation activation as measured by plasma d-dimers and lung function. Methodology/Principal Findings We conducted a cross-sectional study on 2463 randomly selected adults in 1991 and followed up 1252 of these individuals in 2000. Plasma D-dimer levels, a marker of activity of blood coagulation pathways, were analysed in the baseline 1991 samples. There was an inverse cross-sectional association between plasma D-dimer and Forced Expiratory Volume in one second, with a decrease of 71 ml per µg FEU/ml increment in plasma D-dimer (95% confidence intervals CI: −135 to −6), and a decrease in Forced Vital Capacity (97 ml per µg FEU/ml increase in D-dimer, 95%CI: −170 to −24). These associations were attenuated after adjustment for serum highly sensitive CRP. No association was observed between plasma D-dimer and the decline in lung function between 1991 and 2000. Conclusions/Significance The cross-sectional findings are consistent with the hypothesis that activation of blood coagulation pathways is associated with decreased lung function, and that systemic inflammation may contribute to this relation. However, the lack of an association with decline in lung function suggests that clotting pathways that involve d-dimers may not be a promising therapeutic target for new interventions for respiratory disease.
Synthetic Diether‐linked Cationic Lipids for Gene Delivery

Quaternary ammonium lipids 2a–p, with diether linkages between hydrocarbon chains and their ammonium headgroups, were synthesized as potential vectors for cationic liposome‐mediated gene delivery. Varying the length of carbon chains and quaternary ammonium heads as well as different anionic complexes will enable the study of the structure–function relationships of these cationic lipids in terms of gene delivery properties.
Ultra-wide band sensor networks in oil and gas explorations

Seismic exploration and monitoring for oil and gas reservoirs is a peculiar application that requires a large number (1000-2000 nodes/sqkm) of geophone sensors deployed outdoors over large areas (≥ 40 sqkm) to measure backscattered wave fields from artificial sources. A storage/processing unit or sink node collects the measurements from all the geophones to obtain an image of the sub-surface. The existing cabling system to connect sensors is known to cause inefficiencies, large logistic and weight costs, as well as insufficient flexibility in survey design. Oil companies are therefore expecting that wireless connectivity will provide the enabling technology for future seismic explorations. This application represents a new challenging research area for the wireless community. Early results suggest that current off-the-shelf radio solutions do not guarantee the minimum requirements in terms of system usability and energy consumption, not even for current deployment size. This article presents a tutorial view to introduce the basic principles of seismic acquisition systems that are necessary to define the wireless geophone network specifications. Strict sampling synchronization constraint over large geographic areas, high precision sensor localization, and high data rate are all requirements calling for a scalable network system where Ultra-Wide Band radio transmissions play a key role as the only viable technology.
American Society of Addiction Medicine (ASAM) National Practice Guideline for the Use of Medications in the Treatment of Addiction Involving Opioid Use

The Centers for Disease Control have recently described opioid use and resultant deaths as an epidemic. At this point in time, treating this disease well with medication requires skill and time that are not generally available to primary care doctors in most practice models. Suboptimal treatment has likely contributed to expansion of the epidemic and concerns for unethical practices. At the same time, access to competent treatment is profoundly restricted because few physicians are willing and able to provide it. This “Practice Guideline” was developed to assist in the evaluation and treatment of opioid use disorder, and in the hope that, using this tool, more physicians will be able to provide effective treatment. Although there are existing guidelines for the treatment of opioid use disorder, none have included all of the medications used at present for its treatment. Moreover, few of the existing guidelines address the needs of special populations such as pregnant women, individuals with co-occurring psychiatric disorders, individuals with pain, adolescents, or individuals involved in the criminal justice system. This Practice Guideline was developed using the RAND Corporation (RAND)/University of California, Los Angeles (UCLA) Appropriateness Method (RAM) – a process that combines scientific evidence and clinical knowledge to determine the appropriateness of a set of clinical procedures. The RAM is a deliberate approach encompassing review of existing guidelines, literature reviews, appropriateness ratings, necessity reviews, and document development. For this project, American Society of Addiction Medicine selected an independent committee to oversee guideline development and to assist in writing. American Society of Addiction Medicine's Quality Improvement Council oversaw the selection process for the independent development committee. Recommendations included in the guideline encompass a broad range of topics, starting with the initial evaluation of the patient, the selection of medications, the use of all the approved medications for opioid use disorder, combining psychosocial treatment with medications, the treatment of special populations, and the use of naloxone for the treatment of opioid overdose. Topics needing further research were noted.