Miracle-dz/UniFAR-FTUs huggingface dataset:
A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids

The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of this anterior-most, appendage-bearing segment. While this homology statement implies a putative common mechanism for differentiation of deutocerebral appendages across arthropods, experimental data for deutocerebral appendage fate specification are limited to winged insects. Mandibulates (hexapods, crustaceans and myriapods) bear a characteristic pair of antennae on the deutocerebral segment, whereas chelicerates (e.g. spiders, scorpions, harvestmen) bear the eponymous chelicerae. In such hexapods as the fruit fly, Drosophila melanogaster, and the cricket, Gryllus bimaculatus, cephalic appendages are differentiated from the thoracic appendages (legs) by the activity of the appendage patterning gene homothorax (hth). Here we show that embryonic RNA interference against hth in the harvestman Phalangium opilio results in homeonotic chelicera-to-leg transformations, and also in some cases pedipalp-to-leg transformations. In more strongly affected embryos, adjacent appendages undergo fusion and/or truncation, and legs display proximal defects, suggesting conservation of additional functions of hth in patterning the antero-posterior and proximo-distal appendage axes. Expression signal of anterior Hox genes labial, proboscipedia and Deformed is diminished, but not absent, in hth RNAi embryos, consistent with results previously obtained with the insect G. bimaculatus. Our results substantiate a deep homology across arthropods of the mechanism whereby cephalic appendages are differentiated from locomotory appendages.
Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics

Background: Understanding how sequence variants within healthy genomes are distributed with respect to ethnicity and disease-implicated genes is an essential first step toward establishing baselines for personalized genomic medicine.Methods: In this study, we present an analysis of 10 genomes from healthy individuals of various ethnicities, produced using six different sequencing technologies. In total, these genomes contain more than 34 million single-nucleotide variants.Results: We have analyzed these variants from a clinical perspective, assaying the influence of sequencing technology and ethnicity on prognosis. We have also examined the utility of OMIM and the disease-gene literature for determining the impact of rare, personal variants on an individual's health.Conclusions: Our analyses demonstrate that clinical prognoses are complicated by sequencing platform-specific errors and ethnicity. We show that disease-causing alleles are globally distributed along ethnic lines, with alleles known to be disease causing in Eurasians being significantly more likely to be homozygous in Africans.
To Group or Not to Group? Good Practice for Housing Male Laboratory Mice

Simple Summary Wild mice live in territories inhabited by one adult male, several females, and their offspring. This cannot be replicated in the laboratory, so male mice are usually housed in single-sex groups or individually. However, there can be serious animal welfare problems associated with both these approaches, such as lack of social contact when housed individually or aggression between males when kept in groups. Group housing is widely recommended to give male laboratory mice the opportunity to behave as ‘social animals’, but social stress can be detrimental to the welfare of these animals, even without injurious fighting. All of this can also affect the quality of the science, giving rise to ethical concerns. This review discusses whether it is in the best welfare interests of male mice to be housed in groups, or alone. We conclude that it is not possible to give general recommendations for good practice for housing male laboratory mice, as responses to single- and group-housing can be highly context-dependent. The welfare implications of housing protocols should be researched and considered in each case. Abstract It is widely recommended to group-house male laboratory mice because they are ‘social animals’, but male mice do not naturally share territories and aggression can be a serious welfare problem. Even without aggression, not all animals within a group will be in a state of positive welfare. Rather, many male mice may be negatively affected by the stress of repeated social defeat and subordination, raising concerns about welfare and also research validity. However, individual housing may not be an appropriate solution, given the welfare implications associated with no social contact. An essential question is whether it is in the best welfare interests of male mice to be group- or singly housed. This review explores the likely impacts—positive and negative—of both housing conditions, presents results of a survey of current practice and awareness of mouse behavior, and includes recommendations for good practice and future research. We conclude that whether group- or single-housing is better (or less worse) in any situation is highly context-dependent according to several factors including strain, age, social position, life experiences, and housing and husbandry protocols. It is important to recognise this and evaluate what is preferable from animal welfare and ethical perspectives in each case.
Personal exposure to fine particulate matter and benzo[a]pyrene from indoor air pollution and leukocyte mitochondrial DNA copy number in rural China

Households in Xuanwei and Fuyuan, China, possess hazardous levels of fine particulate matter with an aerodynamic diameter <2.5 microns (PM2.5) and polycyclic aromatic hydrocarbons (PAHs) from coal combustion. Previous studies found that increased exposure to PM2.5 and benzo[a]pyrene (BaP; a PAH) were associated with decreased mitochondrial DNA copy number (mtDNAcn), a marker of oxidative stress. We further evaluated these associations in a cross-sectional study of 148 healthy non-smoking women from Xuanwei and Fuyuan. Personal exposure to PM2.5 and BaP was measured using portable devices. MtDNAcn was measured using qPCR amplification of leukocyte DNA that was collected after air measurements. Linear regression models were used to estimate the associations between personal exposure to PM2.5 and BaP, and mtDNAcn adjusted for age, body mass index (BMI) and fuel type. We found inverse associations between exposure to PM2.5 and BaP, and mtDNAcn. Each incremental log-μg/m3 increase in PM2.5 was associated with a significant decrease in mtDNAcn of -10.3 copies per cell [95% confidence interval (95% CI): -18.6, -2.0; P = 0.02]. Additionally, each log-ng/m3 increase in BaP was associated with a significant decrease in mtDNAcn of -5.4 copies per cell (95% CI: -9.9, -0.8, P = 0.02). Age, BMI, fuel type and coal mine type were not significantly associated with mtDNAcn. Exposure to PM2.5 and BaP may alter mitochondrial dynamics in non-smoking Chinese women. MtDNAcn may be a potential mediator of indoor air pollution on chronic disease development.
Zinc intakes and plasma concentrations in men with osteoporosis: the Rancho Bernardo Study.

BACKGROUND Low zinc intakes and reduced blood zinc concentrations have been reported to be associated with osteoporosis in women. OBJECTIVE The objective was to examine the independent association between dietary zinc and plasma zinc and the association of each with bone mineral density (BMD) and 4-y bone loss in community-dwelling older men. DESIGN Of the original Rancho Bernardo Study subjects, 396 men (age: 45-92 y) completed BMD measurements at baseline in 1988-1992 and 4 y later. Osteoporosis was defined as a BMD > or = 2.5 SDs below the mean for young women (a T-score < or = -2.5). At baseline, dietary intake data were collected by using a standard food-frequency questionnaire, and plasma zinc concentrations were measured by using inductively coupled plasma spectroscopy. RESULTS The mean dietary zinc intake was 11.2 mg, and the mean plasma zinc concentration was 12.7 micromol/L. Plasma zinc was correlated with total zinc intake (diet plus supplements). Dietary zinc intake and plasma zinc concentrations were lower in men with osteoporosis at the hip and spine than in men without osteoporosis at those locations. BMDs for the hip, spine, and distal wrist were significantly lower in men in the lowest plasma zinc quartile (<11.3 micromol/L) than in men with higher plasma zinc concentrations. The association between plasma zinc and BMD was cross-sectional, longitudinal, and independent of age or body mass index. However, plasma zinc did not predict bone loss during the 4-y interval. CONCLUSION Dietary zinc intake and plasma zinc each have a positive association with BMD in men.
The Anti-Inflammatory and Antioxidant Potential of Pistachios (Pistacia vera L.) In Vitro and In Vivo

Several reports have demonstrated the effectiveness of pistachio against oxidative stress and inflammation. In this study, we investigate if polyphenols extracts from natural raw shelled pistachios (NP) or roasted salted pistachio (RP) kernels have anti-inflammatory and antioxidant properties at lower doses than reported previously, in both in vitro and in vivo models. The monocyte/macrophage cell line J774 was used to assess the extent of protection by NP and RP pistachios against lipopolysaccharide (LPS)-induced inflammation. Moreover, antioxidant activity of NP and RP was assessed in an in vivo model of paw edema in rats induced by carrageenan (CAR) injection in the paw. Results from the in vitro study demonstrated that pre-treatment with NP (0.01, 0.1 and 0.5 mg/mL) and RP (0.01 and 0.1 mg/mL) exerted a significant protection against LPS induced inflammation. Western blot analysis showed NP reduced the degradation of IκB-α, although not significantly, whereas both NP and RP decreased the TNF-α and IL-1β production in a dose-dependent way. A significant reduction of CAR-induced histological paw damage, neutrophil infiltration and nitrotyrosine formation was observed in the rats treated with NP. These data demonstrated that, at lower doses, polyphenols present in pistachios possess antioxidant and anti-inflammatory properties. This may contribute toward a better understanding of the beneficial health effects associated with consumption of pistachios.
Influence of Starch-Degrading Enzyme on Properties of Cotton Fabrics in In Situ Bleaching Process

Enzymes including starch-degrading enzymes and glucose oxidase are used in one-bath process to desize and bleach cotton fabrics. The effect of enzyme concentration on pretreatment efficiency, especially bleaching of cotton fabrics has been investigated by innovatively focusing on glucose conversion ratio of desizing products. The results showed that the starch sizing materials of cotton fabrics were completely removed by starch-degrading enzymes. The conversion ratio of glucose in desized liquor increased with concentration of glucoamylase. Consequently, whiteness of cotton fabrics bleached in one-bath process was also improved, and an increase of 7% in whiteness of bleached fabrics was observed. The fabric tear strength was decreased. However, the loss ratio could be controlled below 15%. The properties of softness and adsorption of bleached cotton fabrics were satisfactory.
AN AIS-INSPIRED ARCHITECTURE FOR ALERT CORRELATION

There are many different approaches to alert correlation such as using corre- lation rules and prerequisite-con sequences, using machine learning and statistical methods and using similarity measures. In this paper, iCorrelator, a new AIS-inspired architec- ture, is presented. It uses a three-layer architecture that is inspired by three types of responses in the human immune system: the innate immune system's response, the adap- tive immune system's primary response, and the adaptive immune system's secondary response. In comparison with other correlators, iCorrelator does not need information about different attacks and their possible relations in order to discover an attack scenario. It uses a very limited number of general rules that are not related to any specic attack scenario. A process of incremental learning is used to encounter new attacks. Therefore, iCorrelator is easy to set up and work dynamically without reconguration. As a result of using memory cells and improved alert selection policy, the computational cost of iCorre- lator is also acceptable even for online correlation. iCorrelator is evaluated by using the DARPA 2000 dataset and a netForensics honeynet data. The completeness, soundness, false correlation rate and execution time are reported. Results show that iCorrelator is able to extract the attack graphs with acceptable accuracy that is comparable to the best known solutions. Keywords: Intrusion detection system (IDS), Alert correlation, Articial immune sys- tem (AIS)
APPLICATION OF FRACTIONAL DERIVATIVES TO MODELING THE QUASI-STATIC RESPONSE OF POLYURETHANE FOAM

A fractional derivative model of dissipative effects is combined with a nonlinear elastic model to model the response of polyurethane foam in quasi-static compression tests. A system identification method is developed based on a separation of the elastic and viscoelastic parts of the response, which is possible because of symmetries in the imposed deformation timehistory. Simulations are used to evaluate the proposed identification method when noise is present in the response. The system identification technique is also applied with some success to experimental data taken from several compression experiments on two types of polyurethane foam blocks.Copyright © 2003 by ASME
Effects of Striker Shape and Attached Position of Strain Gage on Measured Load in Instrumented Charpy Impact Test

Synopsis : Instrumented Charpy impact test is widely used for the evaluation of toughness of many kinds of materials such as steel, aluminum alloys, polymers and ceramics with small scale specimens. In the test, therefore, it is important to record an accurate impact load. Generally, one can obtain measured load in the instrumented Charpy impact test by multiplying the output signal from strain gage attached to the instrumented striker by load-calibration factor assuming a liner relationship between the strain gage signal and applied load. Although JIS or ISO describes about the instrumented striker, amplifier, data processing parameter and etc., detailed method on load measurement is hardly described in any standard. In the present study, two types of striker were used. The strain gages were attached to 4 positions in each striker. Instrumented Charpy impact test was carried out using these strikers in order to investigate the effect of gage position on actual impact load. By the finite element analysis, the effect of the strain gage position on the measured load was also investigated. As the result, it became clear that the accurate impact load was not measured around the end of slit which was introduced to release the constraining effect of deformation of the gage position from surrounding hammer; the effect of the vibration of the hammer appeared strongly around this position. However, it was possible to prevent the effect of such vibration by attaching the gage away from such position.
Obstructive Sleep Apnea in a rat model: Effects of anesthesia on autonomic evaluation from heart rate variability measures

Rat model of Obstructive Sleep Apnea (OSA) is a realistic approach for studying physiological mechanisms involved in sleep. Rats are usually anesthetized and autonomic nervous system (ANS) could be blocked. This study aimed to assess the effect of anesthesia on ANS activity during OSA episodes. Seven male Sprague-Dawley rats were anesthetized intraperitoneally with urethane (1g/kg). The experiments were conducted applying airway obstructions, simulating 15s-apnea episodes for 15 minutes. Five signals were acquired: respiratory pressure and flow, SaO2, ECG and photoplethysmography (PPG). In total, 210 apnea episodes were studied. Normalized power spectrum of Pulse Rate Variability (PRV) was analyzed in the Low Frequency (LF) and High Frequency (HF) bands, for each episode in consecutive 15s intervals (before, during and after the apnea). All episodes showed changes in respiratory flow and SaO2 signal. Conversely, decreases in the amplitude fluctuations of PPG (DAP) were not observed. Normalized LF presented extremely low values during breathing (median=7,67%), suggesting inhibition of sympathetic system due to anesthetic effect. Subtle increases of LF were observed during apnea. HRV and PPG analysis during apnea could be an indirect tool to assess the effect and deep of anesthesia.
Consumer-centric service-oriented architecture: a new approach

This paper extends the current service-oriented architecture (SOA) to introduce a consumer-centric service-oriented architecture (CCSOA) paradigm. The current SOA is producer-centric, because the basic idea is that service providers publish services that they produce and let the consumers to search available services to compose their applications. CCSOA focuses on consumers' publishing the services they need and even the applications they need. The service providers must produce services that are in need. This new paradigm extends the design and code sharing, and thus further improves the software productivity. This paper presents the concepts, architecture, enabling techniques, and illustrative examples
Development of Avian External Genitalia: Interspecific Differences and Sexual Differentiation of the Male and Female Phallus

Avian genitalia, particularly in waterfowl, are extremely diverse. Penis morphology varies among species, and penis length and elaboration are associated with the frequency of forced extra-pair copulations, yet the developmental mechanisms responsible for this variation are unknown. In addition, females have a small phallic structure that is homologous to the male phallus, but little is known about when or how sexual differentiation takes place. To determine whether species-specific genital morphologies and sexual differentiation occur during duck embryonic development, we characterized development from the onset of genital tubercle initiation through stages of sexual differentiation in 3 species. Pekin and Laysan ducks have long, thick penises, whereas those of Mandarin ducks are shorter and thinner. Development of the genital tubercle is similar throughout the pre-hatching period across the 3 species, suggesting that differences in penis morphology arise post-hatching. We observed that male and female phallus development is similar at early stages, but the female phallus later regresses. Then, we compared male and female genital development between ducks and chickens, which develop a non-intromittent penis. We found that external genital development in male and female chickens resembles that of female ducks, which raises the possibility that male phallus development became feminized during galliform evolution.
Brain ganglioside and glycoprotein sialic acid in breastfed compared with formula-fed infants.

BACKGROUND The concentration of sialic acid in brain gangliosides and glycoproteins has been linked to learning ability in animal studies. Human milk is a rich source of sialic acid-containing oligosaccharides and is a potential source of exogenous sialic acid. OBJECTIVE The aim of the study was to compare the sialic acid concentration in the brain frontal cortex of breastfed and formula-fed infants. DESIGN Twenty-five samples of frontal cortex derived from infants who died of sudden infant death syndrome were analyzed. Twelve infants were breastfed, 10 infants were formula-fed, and 1 infant was mixed-fed; the feeding status of the remaining 2 infants was unknown. Ganglioside-bound and protein-bound sialic acid were determined by HPLC. Ganglioside ceramide fatty acids were also analyzed to determine the relation between sialic acid and long-chain polyunsaturated fatty acids. RESULTS After adjustment for sex with age at death as a covariate, ganglioside-bound and protein-bound sialic acid concentrations were 32% and 22% higher, respectively, in the frontal cortex gray matter of breastfed infants than in that of formula-fed infants (P < 0.01). Protein-bound sialic acid increased with age in both groups (P = 0.02). In breastfed but not in formula-fed infants, ganglioside-bound sialic acid correlated significantly with ganglioside ceramide docosahexaenoic acid and total n-3 fatty acids. CONCLUSIONS Higher brain ganglioside and glycoprotein sialic acid concentrations in infants fed human milk suggests increased synaptogenesis and differences in neurodevelopment.
Pertussis Toxin Exploits Host Cell Signaling Pathways Induced by Meningitis-Causing E. coli K1-RS218 and Enhances Adherence of Monocytic THP-1 Cells to Human Cerebral Endothelial Cells

Pertussis toxin (PTx), the major virulence factor of the whooping cough-causing bacterial pathogen Bordetella pertussis, permeabilizes the blood–brain barrier (BBB) in vitro and in vivo. Breaking barriers might promote translocation of meningitis-causing bacteria across the BBB, thereby facilitating infection. PTx activates several host cell signaling pathways exploited by the neonatal meningitis-causing Escherichia coli K1-RS218 for invasion and translocation across the BBB. Here, we investigated whether PTx and E. coli K1-RS218 exert similar effects on MAPK p38, NF-κB activation and transcription of downstream targets in human cerebral endothelial TY10 cells using qRT-PCR, Western blotting, and ELISA in combination with specific inhibitors. PTx and E. coli K1-RS218 activate MAPK p38, but only E. coli K1-RS218 activates the NF-κB pathway. mRNA and protein levels of p38 and NF-κB downstream targets including IL-6, IL-8, CxCL-1, CxCL-2 and ICAM-1 were increased. The p38 specific inhibitor SB203590 blocked PTx-enhanced activity, whereas E. coli K1-RS218’s effects were inhibited by the NF-κB inhibitor Bay 11-7082. Further, we found that PTx enhances the adherence of human monocytic THP-1 cells to human cerebral endothelial TY10 cells, thereby contributing to enhanced translocation. These modulations of host cell signaling pathways by PTx and meningitis-causing E. coli support their contributions to pathogen and monocytic THP-1 cells translocation across the BBB.