Miracle-dz/UniFAR-FTUs huggingface dataset:
Are Lamarkisms and Darvinisms Suggestions About Evolutionary Process a Problem of the Present Day? Is the Evolution Blind or It is Due to Physical Fields as Information Field?

Grounds for theory: Primo Vascular System (PVS) is a new anatomical and primordial system with unexpected morphological special features, body distribution and functional mechanisms which could be involved to the evolutionary processes. We can speculate and suppose that the DNA as a whole and the DNA granules in PVS’s microcells in particular, carry not only genetic information but its structure is capable to store and transform the information obtained by environment physical fields. The physicists offer the possibility of converting the information to energy and present their findings as a spiral-staircase. As the bases of the DNA lie horizontally between two spiraling strands, the most important in biology molecule of DNA is a spiral model which is able to convert information into energy and vice versa, energy into information on spiral-staircase DNA structure. We suggest that PVS, as a primordial body system distributing through the entire organisms and is connection from surrounding energy fields and every cell of the body. PVS is capable to bring and store information transforming from environmental fields which permits dramatic and sudden “jump”-changing of the organism’s DNA, cells and organisms as a whole. The sudden changing of organisms may explain why there are not enough proofs for intermediate forms between the species and evolution could be logical process due to external signals and influences. Possible effects of theory: Involving of PVS in the evolutionary process as connection between external energies (as electromagnetic field and even information field) with every small part of living organisms as their DNA molecules can explain why the evolution could be a logical process based on the influence of the different physical fields to every cell by transforming energy to information throughout DNA which permits complex “evolutionary jumping” of the organisms. It is possible vice versa process which is able to provoke changes based on influence of internal signals as products of metabolic processes, as well as bio-electrical, bio-luminous and acoustical signals. The acoustical signals could be products of the movement of the internal organs, the muscles, the tendons, the sphincters and valves, too. All internal physical fields bring information concerning indications about the level of the bioprocesses to the PVS web and the organisms react both to the external and internal normal and pathological changes. Conclusion: Our speculations lead to conclusion that PVS could be not only primordial anatomical system but PVS lay at the bottom of the evolution of the living organisms.
The History of Mycoplasma pneumoniae Pneumonia

In the United States in the 1930s, although the pathogen was not known, atypical pneumonia was clinically distinguished from pneumococcal pneumonia by its resistance to sulfonamides. Reimann (1938) reported seven patients with an unusual form of tracheo bronchopneumonia and severe constitutional symptoms. He believed the clinical picture of this disease differed from that of the disease caused by influenza viruses or known bacteria and instead suspected “primary atypical pneumonia. ” For many years, the responsible infectious agent was tentatively classified as a filterable virus that could pass through a Seitz filter to remove bacteria and was reported to be a psittacosis-like or new virus. After that, Eaton et al. (1942, 1944, 1945) identified an agent that was the principal cause of primary atypical pneumonia using cotton rats, hamsters, and chick embryos. Eaton et al. (1942, 1944, 1945) did not perform an inoculation study in human volunteers. During the 1940s, there were three groups engaged in discovering the etiology of the primary atypical pneumonia. (1) Commission on Acute Respiratory Diseases Diseases directed by John Dingle, (2) Dr. Monroe Eaton’s group, the Virus Research Laboratory of the California State Public Health Department, (3) The Hospital of the Rockefeller Institute for Medical Research directed by Horsfall. During 1940s, the members of the Commission on Acute Respiratory Diseases concluded that the bacteria-free filtrates obtained from the patients, presumably containing a virus, could induce primary atypical pneumonia in human volunteers via Pinehurst trials. During 1950s, serological approaches for identification of the Eaton agent developed such as Fluorescent-Stainable Antibody, and at the beginning of the1960s, the Eaton agent successfully grew in media, and finally accepted as a cause of primary atypical pneumonia. Thus, technical difficulties with visualizing the agent and failure to recognize the full significance of the Pinehurst transmission experiments resulted in a lapse of 20 years before acceptance of the Eaton agent as Mycoplasma pneumoniae. This review describes the history of M. pneumoniae pneumonia with a special focus on the recognition between the 1930 and 1960s of the Eaton agent as the infectious cause.
Spatio-temporal decomposition, clustering and identification for alert detection in system logs

In this work, we propose an approach based on analyzing the spatio-temporal partitions of a system log, generated by supercomputers consisting of several nodes, for alert detection without employing semantic analysis. In this case, "Spatial" refers to the source of the log event and "Temporal" refers to the time the log event was reported. Our research shows that these spatio-temporal partitions can be clustered to separate normal activity from anomalous activity, with high accuracy. Therefore, our proposed method provides an effective alert detection mechanism.
Autistic traits in the general population: a twin study.

BACKGROUND Recent research has indicated that autism is not a discrete disorder and that family members of autistic probands have an increased likelihood of exhibiting autistic symptoms with a wide range of severity, often below the threshold for a diagnosis of an autism spectrum disorder. OBJECTIVE To examine the distribution and genetic structure of autistic traits in the general population using a newly established quantitative measure of autistic traits, the Social Responsiveness Scale (formerly known as the Social Reciprocity Scale). METHODS The sample consisted of 788 pairs of twins aged 7 to 15 years, randomly selected from the pool of participants in a large epidemiologic study (the Missouri Twin Study). One parent of each pair of twins completed the Social Responsiveness Scale on each child. The data were subjected to structural equation modeling. RESULTS Autistic traits as measured by the Social Responsiveness Scale were continuously distributed and moderately to highly heritable. Levels of severity of autistic traits at or above the previously published mean for patients with pervasive developmental disorder not otherwise specified were found in 1.4% of boys and 0.3% of girls. Structural equation modeling revealed no evidence for the existence of sex-specific genetic influences, and suggested specific mechanisms by which females may be relatively protected from vulnerability to autistic traits. CONCLUSIONS These data indicate that the social deficits characteristic of autism spectrum disorders are common. Given the continuous distribution of these traits, it may be arbitrary where cutoffs are made between research designations of being "affected" vs "unaffected" with a pervasive developmental disorder. The genes influencing autistic traits appear to be the same for boys and girls. Lower prevalence (and severity) of autistic traits in girls may be the result of increased sensitivity to early environmental influences that operate to promote social competency.
The Neural Mechanism for Sleep Initiation in the Mammalian Brain

Many areas of the brain have been implicated in the sleep cycle, but a holistic picture of their involvement is hard, if not impossible, to find. This paper is meant to summarize in relevant detail the major players in sleep initiation in the mammalian brain. The major players in sleep were broken into two categories: sleep-agonists and sleep-antagonists. The sleep-agonist areas are the median pre-optic nucleus, the ventrolateral pre-optic nucleus, and the Pineal Gland; the sleep-antagonist areas are the raphé nucleus, the locus coeruleus, the perifornical lateral hypothalamus, and the tuberomammillary nucleus. Also included in the paper are introductions to sleep and general neural mechanisms; information on Narcolepsy, Hypersomnia, and Insomnia; and a description of the typical American sleep lab.
A Genome-Wide Aberrant RNA Splicing in Patients with Acute Myeloid Leukemia Identifies Novel Potential Disease Markers and Therapeutic Targets

Purpose: Despite new treatments, acute myeloid leukemia (AML) remains an incurable disease. More effective drug design requires an expanded view of the molecular complexity that underlies AML. Alternative splicing of RNA is used by normal cells to generate protein diversity. Growing evidence indicates that aberrant splicing of genes plays a key role in cancer. We investigated genome-wide splicing abnormalities in AML and based on these abnormalities, we aimed to identify novel potential biomarkers and therapeutic targets. Experimental Design: We used genome-wide alternative splicing screening to investigate alternative splicing abnormalities in two independent AML patient cohorts [Dana-Farber Cancer Institute (DFCI) (Boston, MA) and University Hospital de Nantes (UHN) (Nantes, France)] and normal donors. Selected splicing events were confirmed through cloning and sequencing analysis, and than validated in 193 patients with AML. Results: Our results show that approximately 29% of expressed genes genome-wide were differentially and recurrently spliced in patients with AML compared with normal donors bone marrow CD34+ cells. Results were reproducible in two independent AML cohorts. In both cohorts, annotation analyses indicated similar proportions of differentially spliced genes encoding several oncogenes, tumor suppressor proteins, splicing factors, and heterogeneous-nuclear-ribonucleoproteins, proteins involved in apoptosis, cell proliferation, and spliceosome assembly. Our findings are consistent with reports for other malignances and indicate that AML-specific aberrations in splicing mechanisms are a hallmark of AML pathogenesis. Conclusions: Overall, our results suggest that aberrant splicing is a common characteristic for AML. Our findings also suggest that splice variant transcripts that are the result of splicing aberrations create novel disease markers and provide potential targets for small molecules or antibody therapeutics for this disease. Clin Cancer Res; 20(5); 1135–45. ©2013 AACR.
Effect of altering three phonetic features on intelligibility of English as a lingua franca: a Malaysian speaker and Swedish listeners

ABSTRACT Our previous study examined the mutual intelligibility of Malaysian English to Swedish listeners and Swedish English to Malaysian listeners. The results showed that Swedish listeners did not understand the Malaysian speaker well. In the present study, the Malaysian speaker was trained to alter her realization of the word stress, consonant clusters and long vowels in a way that previous research has found intelligible for both native and non-native English speakers. The audible and measurable alteration signiﬁcantly increased the intelligibility of the speaker for Swedish listeners. This indicates that the three phonetic features are important for intelligibility in international contexts and suggests including the word stress in the Lingua Franca Phonetic Core. Moreover, we discuss that Malaysian English being a dialect and Swedish English being a similect may be relevant to their mutual intelligibility and relate the discussion to teaching English pronunciation in countries where English has been localized.
What Happens When There Is Presumptive 50/50 Parenting Time? An Evaluation of Arizona’s New Child Custody Statute

ABSTRACT The current study presents the findings of an evaluation of Arizona’s 2013 revisions to the child custody statutes that directed courts to “maximize” the child’s parenting time with both parents. A state-wide survey of the four family law professions (i.e., conciliation court staff, judges, mental health providers, and attorneys) assessed their perceptions of the law 4 years after implementation. We averaged the ratings across the four professions to obtain a comprehensive perspective that gave equal weight to each profession. Results revealed that the law functions as a rebuttable presumption of equal parenting time; that it is evaluated positively overall and in terms of children’s best interests; that it is has a neutral impact on legal and interparental conflict; and that it has led to small increases in allegations of domestic violence, child abuse, and substance abuse.
Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition

Summary. In molecular biology, the issue of quantifying the similarity between two biological sequences is very important. Past research has shown that word‐based search tools are computationally efficient and can find some new functional similarities or dissimilarities invisible to other algorithms like FASTA. Recently, under the independent model of base composition, Wu, Burke, and Davison (1997, Biometrics53, 1431–1439) characterized a family of word‐based dissimilarity measures that denned distance between two sequences by simultaneously comparing the frequencies of all subsequences of n adjacent letters (i.e., n‐words) in the two sequences. Specifically, they introduced the use of Mahalanobis distance and standardized Euclidean distance into the study of DNA sequence dissimilarity. They showed that both distances had better sensitivity and selectivity than the commonly used Euclidean distance. The purpose of this article is to extend Mahalanobis and standardized Euclidean distances to Markov chain models of base composition. In addition, a new dissimilarity measure based on Kullback–Leibler discrepancy between frequencies of all n‐words in the two sequences is introduced. Applications to real data demonstrate that Kullback–Leibler discrepancy gives a better performance than Euclidean distance. Moreover, under a Markov chain model of order k̂Q for base composition, where k̂Q is the estimated order based on the query sequence, standardized Euclidean distance performs very well. Under such a model, it performs as well as Mahalanobis distance and better than Kullback–Leibler discrepancy and Euclidean distance. Since standardized Euclidean distance is drastically faster to compute than Mahalanobis distance, in a usual workstation/PC computing environment, the use of standardized Euclidean distance under the Markov chain model of order k̂Q of base composition is generally recommended. However, if the user is very concerned with computational efficiency, then the use of Kullback–Leibler discrepancy, which can be computed as fast as Euclidean distance, is recommended. This can significantly enhance the current technology in comparing large datasets of DNA sequences.
Bilingualism and aging

Whether bilingualism acts positively against neurocognitive decline is intensely debated. Although some reasons for it might be ideological, variability in sampling procedures and experimental design represent potential sources of inconsistency among studies. In this paper, we contend that bilingualism renders the extra-years of life of an increasingly long-lived population cognitively healthy, but only under specific conditions such as continuous practice and immersion in bilingual environments. We thus disagree with some authors’ recommendation that bilingualism be removed from consideration as a neuroprotective factor. We suggest, at the same time, that bilingualism should not be treated as axiologically superior to other environmental measures that promise to contrast the progressive loss of functional independence with increasing age. We conclude by emphasizing the need to evaluate the protective effects of L2-learning on the aging brain in a multimodal intervention perspective, thereby dissociating the effects of bilingualism from those of other cognitively stimulating factors.
A PHOTOMETRIC VARIABILITY SURVEY OF FIELD K AND M DWARF STARS WITH HATNet

Using light curves from the HATNet survey for transiting extrasolar planets we investigate the optical broadband photometric variability of a sample of 27, 560 field K and M dwarfs selected by color and proper motion (V − K ≳ 3.0, μ > 30 mas yr−1, plus additional cuts in J − H versus H − KS and on the reduced proper motion). We search the light curves for periodic variations and for large-amplitude, long-duration flare events. A total of 2120 stars exhibit potential variability, including 95 stars with eclipses and 60 stars with flares. Based on a visual inspection of these light curves and an automated blending classification, we select 1568 stars, including 78 eclipsing binaries (EBs), as secure variable star detections that are not obvious blends. We estimate that a further ∼26% of these stars may be blends with fainter variables, though most of these blends are likely to be among the hotter stars in our sample. We find that only 38 of the 1568 stars, including five of the EBs, have previously been identified as variables or are blended with previously identified variables. One of the newly identified EBs is 1RXS J154727.5+450803, a known P = 3.55 day, late M-dwarf SB2 system, for which we derive preliminary estimates for the component masses and radii of M1 = M2 = 0.258 ± 0.008 M☉ and R1 = R2 = 0.289 ± 0.007 R☉. The radii of the component stars are larger than theoretical expectations if the system is older than ∼200 Myr. The majority of the variables are heavily spotted BY Dra-type stars for which we determine rotation periods. Using this sample, we investigate the relations between period, color, age, and activity measures, including optical flaring, for K and M dwarfs, finding that many of the well-established relations for F, G, and K dwarfs continue into the M dwarf regime. We find that the fraction of stars that is variable with peak-to-peak amplitudes greater than 0.01 mag increases exponentially with the V − KS color such that approximately half of field dwarfs in the solar neighborhood with M ≲ 0.2 M☉ are variable at this level. Our data hint at a change in the rotation–activity–age connection for stars with M ≲ 0.25 M☉.
Fetal Mesenchymal Stromal Cells Differentiating towards Chondrocytes Acquire a Gene Expression Profile Resembling Human Growth Plate Cartilage

We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs) differentiating towards chondrocytes as an alternative model for the human growth plate (GP). Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFβ3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development.
Detecting shock waves in cosmological smoothed particle hydrodynamics simulations

We develop a formalism for the identification and accurate estimation of the strength of structure formation shocks during cosmological smoothed particle hydrodynamics simulations. Shocks play a decisive role not only for the thermalization of gas in virializing structures but also for the acceleration of relativistic cosmic rays (CRs) through diffusive shock acceleration. Our formalism is applicable both to ordinary non-relativistic thermal gas, and to plasmas composed of CRs and thermal gas. To this end, we derive an analytic solution to the one-dimensional Riemann shock tube problem for a composite plasma of CRs and thermal gas. We apply our methods to study the properties of structure formation shocks in high-resolution hydrodynamic simulations of the Lambda cold dark matter (� CDM) model. We find that most of the energy is dissipated in weak internal shocks with Mach numbers M ∼ 2 which are predominantly central flow shocks or merger shock waves traversing halo centres. Collapsed cosmological structures are surrounded by external shocks with much higher Mach numbers up to M ∼ 1000, but they play only a minor role in the energy balance of thermalization. This is because of the higher pre-shock gas densities within non-linear structures, and the significant increase of the mean shock speed as the characteristic halo mass grows with cosmic time. We show that after the epoch of cosmic reionization the Mach number distribution is significantly modified by an efficient suppression of strong external shock waves due to the associated increase of the sound speed of the diffuse gas. Invoking a model for CR acceleration in shock waves, we find that the average strength of shock waves responsible for CR energy injection is higher than that for shocks that dominate the thermalization of the gas. This implies that the dynamical importance of shock-injected CRs is comparatively large in the low-density, peripheral halo infalling regions, but is less important for the weaker flow shocks occurring in central highdensity regions of haloes. When combined with radiative dissipation and star formation, our formalism can also be used to study CR injection by supernova shocks, or to construct models for shock-induced star formation in the interstellar medium.
Stable de Sitter vacua from N=2 supergravity

We find extrema of the potential of matter couplings to = 2 supergravity that define de Sitter vacua and no tachyonic modes. There are three essential ingredients in our construction, namely non-Abelian non-compact gaugings, de Roo–Wagemans rotation angles and Fayet–Iliopoulos terms.
Structured Representation of Biomedical Experiments: A Bottom-Up Approach

Scientific publications are currently the only means to disseminate the details of biomedical experiments across the life sciences research community. With the ever increasing volume of scientific publications, life scientists and curators of life science knowledge bases are often confronted with the daunting task of sifting through hundreds of relevant publications to apprise themselves of the latest experimental techniques and research findings in their area of interest. The use of concise, structured annotations to describe the salient features of experiments would alleviate this difficulty. For this purpose, minimum information standards and controlled vocabularies for experiment representation are in development to be used by biologists to annotate their experiments. This paper presents the initial results from a methodology to manually annotate descriptions of experiments in scientific publications; and discusses the utility of these annotations in a bottom-up approach to creating an ontology of biomedical experiments.