Miracle-dz/UniFAR-FTUs huggingface dataset:
Macroscopic folding and replication of the homogeneously staining region in late S phase leads to the appearance of replication bands in mitotic chromosomes

The chromosomal G/R bands are alternating domains differing in their nucleotide sequence biases. The bands are also related to the time of replication: pulse-labeling during S phase makes the replication sites as visible as replication bands that are close to the G/R bands in mitotic chromosomes. We previously showed that a plasmid bearing a mammalian replication origin efficiently generated a chromosomal homogeneously staining region (HSR). Here, we analyze the replication of this artificial HSR and show that it was replicated at the last stage of S phase. The HSR was composed of plasmid repeats only; nonetheless, we found that replication sites pulse-labeled during late S phase appeared as bands in the mitotic HSR and their number was dependent on the length of the HSR. Therefore, replication bands might not arise from sequence information per se. To understand the chronological order of appearance of replication sites, we performed a double pulse-chase experiment using IdU and CldU. Replication of the entire HSR required 100-120 minutes. During this period, the replicated sites appeared as bands at the first and last stages, but in between were apparently scattered along the entire HSR. An analysis of S-phase nuclei revealed that the replication started at the periphery of the globular HSR domain, followed by initiation in the internal domain. The replicated HSR appeared as a ring or a pair of extended spirals in late G2-phase nuclei. To account for these findings, we present a model in which the HSR is folded as a coiled-coil structure that is replicated from the outside to the inside in S phase nuclei.
Investigation of oxidative stress in pterygium tissue

Purpose To investigate changes in the oxidant-antioxidant system in pterygium tissue. Methods Tissue samples ablated from 40 patients during pterygium surgery constituted the study material, while normal nasal conjunctiva tissue samples from 20 patients matched for age group (who had undergone surgery for strabismus or extracapsular cataract surgery) were used as controls. The samples were kept at −70 °C until the time of analysis. Catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) enzymatic activity and the levels of nitric oxide (NO) and malone dialdehyde (MDA) were studied in both groups. Results The mean age was 54.0±12 years in the pterygium patients and 49.0±19 in the controls (p=0.270). The enzyme activity levels were significantly lower in the pterygium group when compared to the controls (p<0.001 in each case), while in the same group a significant increase was observed in the MDA and NO levels (also p<0.001, in both cases). Conclusions These findings indicating oxidative stress in the pterygium tissue suggest that oxidative stress can play a role in pterygium etiopathogenesis.
Improved Source Coding Exponents via Witsenhausen's Rate

We provide a novel upper-bound on Witsenhausen's rate, the rate required in the zero-error analogue of the Slepian-Wolf problem. Our bound is given in terms of a new information-theoretic functional defined on a certain graph and is derived by upper bounding complementary graph entropy. We use the functional, along with graph entropy, to give a single letter lower-bound on the error exponent for the Slepian-Wolf problem under the vanishing error probability criterion, where the decoder has full (i.e., unencoded) side information. We demonstrate that our error exponent can beat the “expurgated” source-coding exponent of Csiszár and Körner for some sources that have zeroes in the “channel” matrix connecting the source with the side information. An extension of our scheme to the lossy case (i.e., Wyner-Ziv) is given. For the case in which the side information is a deterministic function of the source, the exponent of our improved scheme agrees with the sphere-packing bound exactly (thus determining the reliability function). An application of our functional to zero-error channel capacity is also given.
Behavioral Abnormalities in Captive Nonhuman Primates

In this study, we dealt with 11 species of nonhuman primates across 10 zoos in India. We recorded behavior as instantaneous scans between 9 a.m. and 5 p.m. In the study, we segregated behaviors for analyses into abnormal, undesirable, active, and resting. The 4 types of abnormal behavior exhibited included floating limb, self-biting, self-clasping, and stereotypic pacing. In the study, we recorded 2 types of undesirable behavior: autoerotic stimulation and begging. Langurs and group-housed macaques did not exhibit undesirable behaviors. A male lion-tailed macaque and a male gibbon exhibited begging behavior. autoerotic stimulation and self-biting occurred rarely. Males exhibited higher levels of undesirable behavior than did females. Animals confiscated from touring zoos, circuses, and animal traders exhibited higher levels of abnormal behaviors than did animals reared in larger, recognized zoos. The stump-tailed macaque was the only species to exhibit floating limb, autoerotic stimulation, self-biting, and self-clasping. Our results show that rearing experience and group composition influence the proportions of abnormal behavior exhibited by nonhuman primates in captivity. The history of early social and environmental deprivation in these species of captive nonhuman primates probably is critical in the development of behavioral pathologies. Establishing this will require further research.
Green Tea Epigallocatechin-3-Gallate Mediates T Cellular NF-κB Inhibition and Exerts Neuroprotection in Autoimmune Encephalomyelitis1

Recent studies in multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE), point to the fact that even in the early phase of inflammation, neuronal pathology plays a pivotal role in the sustained disability of affected individuals. We show that the major green tea constituent, (−)-epigallocatechin-3-gallate (EGCG), dramatically suppresses EAE induced by proteolipid protein 139–151. EGCG reduced clinical severity when given at initiation or after the onset of EAE by both limiting brain inflammation and reducing neuronal damage. In orally treated mice, we found abrogated proliferation and TNF-α production of encephalitogenic T cells. In human myelin-specific CD4+ T cells, cell cycle arrest was induced, down-regulating the cyclin-dependent kinase 4. Interference with both T cell growth and effector function was mediated by blockade of the catalytic activities of the 20S/26S proteasome complex, resulting in intracellular accumulation of IκB-α and subsequent inhibition of NF-κB activation. Because its structure implicates additional antioxidative properties, EGCG was capable of protecting against neuronal injury in living brain tissue induced by N-methyl-d-aspartate or TRAIL and of directly blocking the formation of neurotoxic reactive oxygen species in neurons. Thus, a natural green tea constituent may open up a new therapeutic avenue for young disabled adults with inflammatory brain disease by combining, on one hand, anti-inflammatory and, on the other hand, neuroprotective capacities.
North African Populations Carry the Signature of Admixture with Neandertals

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.
Laboratory indicators of mastitis are not associated with elevated HIV-1 DNA loads or predictive of HIV-1 RNA loads in breast milk.

BACKGROUND Mother-to-child transmission (MTCT) of HIV-1 has been associated with symptomatic and asymptomatic mastitis and with the quantity of HIV-1 RNA and DNA in maternal milk. An improved understanding of the relationship between indicators of inflammation and HIV-1 loads in breast milk could improve MTCT prevention strategies. METHODS In a cross-sectional study, laboratory indicators of mastitis (breast milk sodium [Na(+)] concentration, sodium : potassium ratio [Na(+) : K(+)], and leukocyte count) were related to breast milk HIV-1 RNA and DNA loads and were evaluated for predicting viral loads in milk. RESULTS Mastitis was present in 63 (15%) of 407, 60 (15%) of 407, and 76 (18%) of 412 milk specimens, as defined by Na(+) concentration >12 mmol/L, Na(+) : K(+) >1, and total leukocyte counts > or =10(6) cells/mL, respectively. Each indicator was associated with an increased milk HIV-1 RNA load (P<.05) but not with HIV-1 DNA load. Neutrophils correlated better with milk HIV-1 RNA load than total leukocytes. However, neither neutrophil count, Na(+) concentration, nor Na(+) : K(+) displayed a threshold that was both sensitive and specific for the detection of HIV-1 RNA in milk at thresholds of > or =50 or > or =10(4) copies/mL. CONCLUSIONS HIV-1 DNA loads in breast milk were not increased during mastitis. Neither milk cell counts nor electrolyte concentrations were useful predictors of milk HIV-1 RNA or DNA loads for individual women.
Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework

The order Botryosphaeriales represents several ecologically diverse fungal families that are commonly isolated as endophytes or pathogens from various woody hosts. The taxonomy of members of this order has been strongly influenced by sequence-based phylogenetics, and the abandonment of dual nomenclature. In this study, the phylogenetic relationships of the genera known from culture are evaluated based on DNA sequence data for six loci (SSU, LSU, ITS, EF1, BT, mtSSU). The results make it possible to recognise a total of six families. Other than the Botryosphaeriaceae (17 genera), Phyllostictaceae (Phyllosticta) and Planistromellaceae (Kellermania), newly introduced families include Aplosporellaceae (Aplosporella and Bagnisiella), Melanopsaceae (Melanops), and Saccharataceae (Saccharata). Furthermore, the evolution of morphological characters in the Botryosphaeriaceae were investigated via analysis of phylogeny-trait association. None of the traits presented a significant phylogenetic signal, suggesting that conidial and ascospore pigmentation, septation and appendages evolved more than once in the family. Molecular clock dating on radiations within the Botryosphaeriales based on estimated mutation rates of the rDNA SSU locus, suggests that the order originated in the Cretaceous period around 103 (45-188) mya, with most of the diversification in the Tertiary period. This coincides with important periods of radiation and spread of the main group of plants that these fungi infect, namely woody Angiosperms. The resulting host-associations and distribution could have influenced the diversification of these fungi. Taxonomic novelties: New families - Aplosporellaceae Slippers, Boissin & Crous, Melanopsaceae Phillips, Slippers, Boissin & Crous, Saccharataceae Slippers, Boissin & Crous.
Barriers to expanding advanced pharmacy practice experience site availability in an experiential education consortium.

OBJECTIVES To compare 2006-2007 and projected 2010-2011 advanced pharmacy practice experience (APPE) availability and needs for 4 colleges and schools of pharmacy in Georgia and Alabama and to examine barriers and offer potential solutions to increase APPE site and preceptor availability. METHODS Data on APPE needs and availability were gathered prospectively and evaluated relative to current and projected enrollment and planned programmatic changes. RESULTS Combined 2006-2007 non-community APPE needs and availabilities were 3,590 and 4,427, respectively, with a surplus availability of 837. Combined projected 2010-2011 non-community APPEs were estimated at 4,309. Assuming 2006-2007 non-community availability remained unchanged, the surplus availability declined to 118. CONCLUSIONS The need for quality experiential education represents a significant barrier and rate-limiting step to the matriculation of the increased numbers of pharmacists. Barriers to expanding APPE availability include: introductory pharmacy practice experience (IPPE) and APPE expansion, growth of new and existing pharmacy programs, financial instability of acute care facilities, and lack of preceptor development resources. Regional experiential education consortiums can provide a constructive approach to improve access to quality sites and preceptors through standardizing processes and leveraging resources.
Towards a theory of statistical tree-shape analysis

In order to develop statistical methods for shapes with a tree-structure, we construct a shape space framework for tree-like shapes and study metrics on the shape space. This shape space has singularities, corresponding to topological transitions in the represented trees. We study two closely related metrics on the shape space, TED and QED. QED is a quotient Euclidean distance arising naturally from the shape space formulation, while TED is the classical tree edit distance. Using Gromov's metric geometry we gain new insight into the geometries defined by TED and QED. We show that the new metric QED has nice geometric properties which facilitate statistical analysis, such as existence and local uniqueness of geodesics and averages. TED, on the other hand, does not share the geometric advantages of QED, but has nice algorithmic properties. We provide a theoretical framework and experimental results on synthetic data trees as well as airway trees from pulmonary CT scans. This way, we effectively illustrate that our framework has both the theoretical and qualitative properties necessary to build a theory of statistical tree-shape analysis.
On Ontology, ontologies, Conceptualizations, Modeling Languages, and (Meta)Models

In philosophy, the term ontology has been used since the 17th century to refer both to a philosophical discipline (Ontology with a capital “O”), and as a domain-independent system of categories that can be used in the conceptualization of domain-specific scientific theories. In the past decades there has been a growing interest in the subject of ontology in computer and information sciences. In the last few years, this interest has expanded considerably in the context of the Semantic Web and MDA (Model-Driven Architecture) research efforts, and due to the role ontologies are perceived to play in these initiatives. In this paper, we explore the relations between Ontology and ontologies in the philosophical sense with domain ontologies in computer science. Moreover, we elaborate on formal characterizations for the notions of ontology, conceptualization and metamodel, as well as on the relations between these notions. Additionally, we discuss a set of criteria that a modeling language should meet in order to be considered a suitable language to model phenomena in a given domain, and present a systematic framework for language evaluation and design. Furthermore, we argue for the importance of ontology in both philosophical senses aforementioned for designing and evaluating a suitable general ontology representation language, and we address the question whether the so-called Ontology Web languages can be considered as suitable general ontology representation languages. Finally, we motivate the need for two complementary classes of modeling languages in Ontology Engineering addressing two separate sets of concerns.
The Importance of Music in Preschool Education.

At a few universities in Sweden students can chose a preschool teacher education programme with a music profile. At one of these universities, a study was undertaken that aimed to explore student teachers' understanding of self as musician, their future professional role as a preschool teacher and how the education equips for that. Sixteen students participated in focus group interviews, and thirty students answered a questionnaire. The study shows that almost three-quarters of the students did not choose the music profile for the sake of the specific profile in music. Instead, it happened that this was the programme they managed to get into or they found the location of the education suitable. How, then, to develop the design of a music profile that prepares preschool teacher students to become skilled leaders and a source of inspiration for music in preschools?
Fabrication and Biocompatibility of Electrospun Silk Biocomposites

Silk fibroin has attracted great interest in tissue engineering because of its outstanding biocompatibility, biodegradability and minimal inflammatory reaction. In this study, two kinds of biocomposites based on regenerated silk fibroin are fabricated by electrospinning and post-treatment processes, respectively. Firstly, regenerated silk fibroin/tetramethoxysilane (TMOS) hybrid nanofibers with high hydrophilicity are prepared, which is superior for fibroblast attachment. The electrospinning process causes adjacent fibers to ‘weld’ at contact points, which can be proved by scanning electron microscope (SEM). The water contact angle of silk/tetramethoxysilane (TMOS) composites shows a sharper decrease than pure regenerated silk fibroin nanofiber, which has a great effect on the early stage of cell attachment behavior. Secondly, a novel tissue engineering scaffold material based on electrospun silk fibroin/nano-hydroxyapatite (nHA) biocomposites is prepared by means of an effective calcium and phosphate (Ca–P) alternate soaking method. nHA is successfully produced on regenerated silk fibroin nanofiber within several min without any pre-treatments. The osteoblastic activities of this novel nanofibrous biocomposites are also investigated by employing osteoblastic-like MC3T3-E1 cell line. The cell functionality such as alkaline phosphatase (ALP) activity is ameliorated on mineralized silk nanofibers. All these results indicate that this silk/nHA biocomposite scaffold material may be a promising biomaterial for bone tissue engineering.
A general mortality study of production workers in the paint and coatings manufacturing industry. A preliminary report.

Information has been obtained on a cohort of 16,243 men employed for at least one year in the manufacture of paint or vanish after January 1, 1946, and for seven subgroups on the basis of exposure. These workers experienced a level of mortality that compares favorably with that of the U.S. white male population. The workers' pattern of mortality differed somewhat from the U.S. pattern, with considerably reduced mortality from psychiatric, metabolic, respiratory, and violent causes. There was an increased mortality due to bowel and rectal cancer. While the numbers are smaller, there are also increased rates for liver and skin cancer. Lung cancer rates, while not in excess of the national average, did not match the low mortality from nonmalignant, noninfectious respiratory disease. The authors have concluded that work in this industry presents no major health hazard.
Learning Word Meanings and Descriptive Parameter Spaces from Music

The audio bitstream in music encodes a high amount of statistical, acoustic, emotional and cultural information. But music also has an important linguistic accessory; most musical artists are described in great detail in record reviews, fan sites and news items. We highlight current and ongoing research into extracting relevant features from audio and simultaneously learning language features linked to the music. We show results in a "query-by-description" task in which we learn the perceptual meaning of automatically-discovered single-term descriptive components, as well as a method of automatically uncovering 'semantically attached' terms (terms that have perceptual grounding.) We then show recent work in 'semantic basis functions' --- parameter spaces of description (such as fast . slow or male . female) that encode the highest descriptive variance in a semantic space.
Finding Words and Rules in a Speech Stream

We have proposed that consonants give cues primarily about the lexicon, whereas vowels carry cues about syntax. In a study supporting this hypothesis, we showed that when segmenting words from an artificial continuous stream, participants compute statistical relations over consonants, but not over vowels. In the study reported here, we tested the symmetrical hypothesis that when participants listen to words in a speech stream, they tend to exploit relations among vowels to extract generalizations, but tend to disregard the same relations among consonants. In our streams, participants could segment words on the basis of transitional probabilities in one tier and could extract a structural regularity in the other tier. Participants used consonants to extract words, but vowels to extract a structural generalization. They were unable to extract the same generalization using consonants, even when word segmentation was facilitated and the generalization made simpler. Our results suggest that different signal-driven computations prime lexical and grammatical processing.
Specification versus reality: Experimental evaluation of link capacity estimation in IEEE 802.11

Many wireless network protocols and algorithms rely on estimations of the link capacity in order to make informed decisions on routing data packets, selection of the optimal transmission rate, flow and admission control. In this paper we present an investigation into our Effective Link Capacity (ELC) metric which combines the use of MAC layer monitoring with knowledge of the network timing specifications to provide an accurate model of link conditions. We subject the resulting metric to an experimental investigation across a range of conditions using a conducted testbed. We demonstrate that commodity wireless devices do not conform to the IEEE 802.11 specification, thus making modeling difficult. Given that ELC and the IEEE 802.11s Airtime link metric are directly related, we compare their accuracy in estimating the link capacity. We demonstrate that ELC significantly outperforms two widely-used implementations of Airtime.
Decreased expression of DARPP-32 in oral premalignant and malignant lesions.

BACKGROUND DARPP-32 is a neuronal protein that plays a central role in dopaminergic neurotransmission. Although DARPP-32 may contribute to the pathogenesis of several human malignancies, its expression has never been investigated in oral premalignant and malignant lesions. MATERIALS AND METHODS DARPP-32 expression was examined using immunohistochemistry in 14 normal oral mucosa, 5 normal lower lip mucosa, 41 oral leukoplakia (OL), 30 oral squamous cell carcinoma (OSCC) and 20 lower lip squamous cell carcinoma (LLSCC) specimens. Differences of its expression between groups were analyzed. RESULTS OSCC and OL with moderate or severe dysplasia showed lower DARPP-32 expression in relation to normal oral mucosa. LLSCC showed lower DARPP-32 expression than normal lower lip mucosa and OSSC. CONCLUSION The decreased expression of DARPP-32 in oral premalignant and malignant lesions suggests a tumor suppressor role for this protein in the tumorigenesis of these lesions.