Miracle-dz/UniFAR-FTUs huggingface dataset:
The Relationship of Suicidal Ideation to Objective and Subjective Executive Functioning

Prior research on executive ability and suicidal ideation (SI) has frequently failed to account for either symptom or performance validity. Similarly, studies have not adequately examined both objective performance on executive tests and subjective report of executive deficits in relationship to SI. The purpose of this study was to address these gaps in research by accounting for performance validity, symptom validity, and considering self-reported executive complaints with objective performance. We hypothesized that (a) increases in self-reported SI on the Personality Assessment Inventory (PAI; Morey, 1991) Suicidal Ideation subscale would be related to poorer performance on objective and subjective tests of executive function and (b) level of self-reported depressive symptoms would moderate the relationship between SI and measures of executive function, such that individuals with higher levels of both depressive symptoms and executive dysfunction would be more likely to experience higher levels of SI. No measure of executive function was related to SI when accounting for demographic variables and depressive symptoms. Wisconsin Card Sort Test categories completed was the only measure of executive function to interact significantly with depressive symptoms to predict SI (β = .43). Of particular note, self-reported executive dysfunction was highly correlated with Beck Depression Inventory−II ( Beck, Steer, & Brown, 1996) scores (r = .78). Clinical implications and future directions for research are discussed.
Do socio-economic inequalities in infant growth in rural India operate through maternal size and birth weight?

Abstract Background: In total, 3.1 million young children die every year from under-nutrition. Greater understanding of associations between socio-economic status (SES) and the biological factors that shape under-nutrition are required to target interventions. Aim: To establish whether SES inequalities in under-nutrition, proxied by infant size at 12 months, operate through maternal and early infant size measures. Subjects and methods: The sample comprised 347 Indian infants born in 60 villages in rural Andhra Pradesh 2005–2007. Structural equation path models were applied to decompose the total relationship between SES (standard of living index) and length and weight for age Z-scores (LAZ/WAZ) at 12 months into direct and indirect (operating through maternal BMI and height, birthweight Z-score and LAZ/WAZ at 6 months) paths. Results: SES had a direct positive association with LAZ (Standardised coefficient = 0.08, 95% CI = 0.02–0.13) and WAZ at age 12 months (Standardised coefficient = 0.08, 95% CI = 0.02–0.15). It also had additional indirect positive associations through increased maternal height and subsequently increased birthweight and WAZ/LAZ at 6 months, accounting for 35% and 53% of the total effect for WAZ and LAZ, respectively. Conclusion: Findings support targeting evidence based growth interventions towards infants from the poorest families with the shortest mothers. Increasing SES can improve growth for two generations.
Risk of rheumatoid arthritis development in patients with unclassified arthritis according to the 2010 ACR/EULAR criteria for rheumatoid arthritis.

OBJECTIVE Early recognition and treatment of RA is associated with an improved outcome. The 2010 ACR/EULAR criteria for RA identify RA patients earlier than the 1987 ACR criteria. Nevertheless, we recently observed that 24% of the 2010 unclassified arthritis (UA) patients develop RA during follow-up. Here we studied this frequency in other cohorts and evaluated the prognostic accuracy of ACPA and the Leiden prediction rule in 2010 UA patients. METHODS The 2010 UA patients from three Early Arthritis Clinics were studied: 776 from Leiden, 121 from Birmingham and 322 from Amsterdam. Fulfilment of the 1987 ACR criteria during follow-up was studied as the primary outcome. DMARD prescription during the year and having a persistent course of arthritis over 7 years were studied as secondary outcomes in one cohort. The presence of ACPA and the prediction score at baseline were evaluated in relation to these outcomes. RESULTS In the three cohorts, 24%, 26% and 12%, respectively, of the 2010 UA patients fulfilled the 1987 criteria after 1 year. However, some of these patients already fulfilled the 1987 criteria at baseline. In 1987 and 2010 UA patients, 15%, 21% and 9%, respectively, developed RA (1987) at 1 year. In these patients, 0-6% of the patients were ACPA positive and 0-1% had high prediction scores. Consequently a large majority of the UA patients with an unfavourable outcome was not recognized by these prognostic tools. CONCLUSION A proportion of 2010 UA patients progress to RA. ACPA and the Leiden prediction rule are not useful in identifying these patients. These results imply that other predictive markers should be developed for 2010 UA patients.
Endoplasmic reticulum lectin XTP3‐B inhibits endoplasmic reticulum‐associated degradation of a misfolded α1‐antitrypsin variant

The endoplasmic reticulum (ER) is an organelle that synthesizes many secretory and membrane proteins. However, proteins often fold incorrectly. Terminally misfolded polypeptides in the ER are retro‐translocated to the cytosol, where they are ultimately degraded by the ubiquitin–proteasome system, a process termed ER‐associated degradation (ERAD). By recognizing the specific structures of N‐linked oligosaccharides attached to polypeptides, lectins play an important role in the quality control of glycoproteins in the ER. Mammalian OS‐9 and XTP3‐B are ER‐resident lectins that contain mannose 6‐phosphate receptor homology (MRH) domains, which recognize sugar moieties; OS‐9 has one MRH domain and XTP3‐B has two. Both are involved in ERAD, but the functional differences between the two are poorly understood. The present study analyzed the function of human XTP3‐B, and found, by frontal affinity chromatography analysis, that its C‐terminal MRH domain specifically recognized the Man9GlcNAc2 (M9) glycan in vitro and M9 glycans on an ERAD substrate NHK, a terminally misfolded α1‐antitrypsin variant, in vivo. Furthermore, endogenous XTP3‐B was a component of the HRD1–SEL1L membrane‐embedded ubiquitin ligase complex, an association that was stabilized by a direct interaction with SEL1L. The lectin activity of XTP3‐B was required for its binding to NHK, but not for its association with SEL1L. Unlike OS‐9, XTP3‐B did not enhance the degradation of misfolded glycoproteins, but instead inhibited the degradation of NHK bearing M9 oligosaccharides. Therefore, we propose that XTP3‐B recognizes M9 glycans on unfolded polypeptides, thereby acting as a negative regulator of ERAD, and also protects newly synthesized immature polypeptides from premature degradation.
Characterization of ATP-binding Cassette Transporter Genes in Silkworm, Bombyx Mori

Background: ATP-binding cassette (ABC) transporters are transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) binding and hydrolysis to transport various substrates across extra and intracellular membranes, including metabolic products, lipids and sterols, and drugs. They play important roles in various processes of life, especially in drug resistance, metabolism and development. Objective: Identify the ATP-binding cassette (ABC) transporter gene family and their members in the genome of silkworm, Bombyx mori. Method: Bioinformatics and phylogenetic analysis were used in the study. Results: We identified 47 ABC proteins in the silkworm genome, which possesses members of all current ABC subfamilies A to H. ABC proteins of silkworm were compared to those from worm, fruit fly and human. A high conservation of silkworm ABC transporters were observed for proteins involved in fundamental cellular processes, including the half transporters of the ABCB subfamily, which function in iron metabolism and transport of Fe/S protein precursors, and the members of subfamilies ABCD, ABCE and ABCF, which have roles in very long chain fatty acid transport. Both ABCE and F gene products may be involved in an innate immune response to viral infections. As in the fly, ABCH proteins are inverse half-transporters showing the same domain architecture as the members of the ABCG subfamily, and ABCG transporters involve in transportation of ommochrome precursors and uric acid into pigment granules and urate granules. Conclusion: These results paved the way for further study on the function of the ABC transporters in silkworm, Bombyx mori.
Cortical Differentiation for Nouns and Verbs Depends on Grammatical Markers

Here we address the contentious issue of how nouns and verbs are represented in the brain. The co-occurrence of noun and verb deficits with damage to different neural regions has led to the view that they are differentially represented in the brain. Recent neuroimaging evidence and inconsistent lesionbehavior associations challenge this view. We have suggested that nouns and verbs are not differentially represented in the brain, but that different patterns of neural activity are triggered by the different linguistic functions carried by nouns and verbs. We test these claims in a functional magnetic resonance imaging study using homophoneswords which function grammatically as nouns or verbs but have the same form and meaningensuring that any neural differences reflect differences in grammatical function. Words were presented as single stems and in phrases in which each homophone was preceded by an article to create a noun phrase (NP) or a pronoun to create a verb phrase (VP), thus establishing the word's functional linguistic role. Activity for single-word homophones was not modulated by their frequency of usage as a noun or verb. In contrast, homophones marked as verbs by appearing in VPs elicited greater activity in the left posterior middle temporal gyrus (LpMTG) compared to homophones marked as nouns by occurring in NPs. Neuropsychological patients with grammatical deficits had lesions which overlapped with the greater LpMTG activity found for VPs. These results suggest that nouns and verbs do not invariably activate different neural regions; rather, differential cortical activity depends on the extent to which their different grammatical functions are engaged.
Phenotype Restricted Genome-Wide Association Study Using a Gene-Centric Approach Identifies Three Low-Risk Neuroblastoma Susceptibility Loci

Neuroblastoma is a malignant neoplasm of the developing sympathetic nervous system that is notable for its phenotypic diversity. High-risk patients typically have widely disseminated disease at diagnosis and a poor survival probability, but low-risk patients frequently have localized tumors that are almost always cured with little or no chemotherapy. Our genome-wide association study (GWAS) has identified common variants within FLJ22536, BARD1, and LMO1 as significantly associated with neuroblastoma and more robustly associated with high-risk disease. Here we show that a GWAS focused on low-risk cases identified SNPs within DUSP12 at 1q23.3 (P = 2.07×10−6), DDX4 and IL31RA both at 5q11.2 (P = 2.94×10−6 and 6.54×10−7 respectively), and HSD17B12 at 11p11.2 (P = 4.20×10−7) as being associated with the less aggressive form of the disease. These data demonstrate the importance of robust phenotypic data in GWAS analyses and identify additional susceptibility variants for neuroblastoma.
Mass Isolation of Primordial Germ Cells from Transgenic Rainbow Trout Carrying the Green Fluorescent Protein Gene Driven by the vasa Gene Promoter

Abstract Mass isolation of live primordial germ cells (PGCs) was demonstrated for the first time in ectothermal vertebrates. To establish a stem cell-mediated gene transfer system in fish, a stem cell line that retains the ability to develop into gametes is necessary. PGCs are well suited for use as the initial material for such a stem cell line. We established transgenic rainbow trout (Oncorhynchus mykiss) strains carrying the green fluorescent protein (GFP) gene driven by a rainbow trout vasa-like gene (RtVLG) promoter/enhancer. Because GFP expression was specific to the PGCs, PGCs were successfully visualized in all developmental stages examined. Isolated genital ridges containing GFP-labeled PGCs were enzymatically dissociated. To isolate PGCs from the complex pools of dissociated genital ridges, GFP-labeled cells were sorted by flow cytometry. The sorted GFP-positive cells were large and round with a large nucleus, typical characters of PGC morphology. The expression of RtVLG was detected only in the GFP-positive cell population, confirming that these cells were PGCs. This simple and efficient technique to purify a large number of viable PGCs opens the way for establishing a stem cell line, which can differentiate into the germline. The purified PGCs would also be a novel tool for cellular and molecular study of vertebrate germline stem cells.
Rapid measurement of specific membrane capacitance and cytoplasm conductivity on single cells

This paper presents a technique for the characterization of single-cell electrical properties (specific membrane capacitance and cytoplasm conductivity) at a speed of 5-10 cells per second (vs. minutes per cell using existing techniques). When a cell flows through a microfluidic constriction channel, electrical impedance at multiple frequencies is measured. Electrical and geometrical models were developed to interpret the impedance data and determine the specific membrane capacitance and cytoplasm conductivity of individual cells. Results from testing 3,249 AML-2 cells and 3,398 HL-60 cells reveal different electrical properties between these two cell types. The results also demonstrate that the quantification of specific membrane capacitance and cytoplasm conductivity can enhance cell classification results.
Detectability of Mixed Unburnt C+O in Type Ia Supernova Spectra

Motivated by recent three-dimensional calculations of the explosion of Type Ia supernovae via a pure deflagration, we calculate the observed spectra at 15-25 days past maximum light of a parameterized model that has a considerable fraction of unburnt C+O in the central regions. Rather than attempting a self-consistent three-dimensional calculation, which is beyond the scope of current computer codes, we modify the composition structure of the one-dimensional deflagration model W7. In our exploratory parameterized calculations, we find that a central concentration of C+O is not ruled out by observations for the epochs we study. We briefly examine whether nebular phase spectra could be incompatible with observations.
Transposed-letter effects: Consonants, vowels and letter frequency

There is now considerable evidence (e.g., Perea & Lupker, 2003a, 2003b) that transposed-letter nonword primes (e.g., jugde for JUDGE) are more effective primes than replacement-letter nonword primes (e.g., jupte for JUDGE). Recently, Perea and Lupker (2004) demonstrated that, in Spanish, this transposed-letter prime advantage exists only when the transposed letters are consonants (C-C transpositions) and not when they are vowels (V-V transpositions). This vowel-consonant difference causes problems even for models that can successfully explain transposed-letter effects (e.g., SOLAR, Davis, 1999). In Experiment 1 in the present paper, we demonstrated a parallel result in a language with a different syllabic structure (English) in both a masked priming experiment and an unprimed lexical decision task in which the transposed letter strings (e.g., ADACEMY, ACEDAMY) were used as the nonwords. Results in Experiment 2 suggest that at least part of the reason for the vowel-consonant difference is because of the higher letter frequencies of the vowels. Possible alternative interpretations of the vowel-consonant difference are discussed.
Nicotine and alcohol use in adolescent psychiatric inpatients: Associations with diagnoses, psychosocial factors, gender and age

The aim of the survey was to describe the proportion of smokers and alcohol users in a group of children and adolescents admitted to a German department of child and adolescent psychiatry and psychotherapy. In addition, the proportion of smokers in this group of patients was compared with the proportion in the general population of the same age. The sample was composed of all children and adolescent inpatients (n=432, 8–17years old meeting inclusion criteria) admitted to a German department of child and adolescent psychiatry between May 2001 and June 2003. A shortened adaptation of the questionnaire on legal and illegal drug use, developed by the Swiss Professional Service for Alcohol Problems, Lausanne, was used. Initiation, frequency and quantity of drug use, and parental substance use were assessed. The results showed an association between conduct disorder (CD) and attention-deficit/hyperactivity disorder (ADHD) and an early initiation of nicotine and alcohol use. Girls and boys with CD and ADHD were significantly more likely to be involved in higher levels of nicotine use compared with the general population. Parental nicotine use was associated with smoking in girls, while maternal nicotine use was associated with smoking in boys. Furthermore, regular alcohol use in both girls and boys was associated with nicotine use. To conclude, early initiation and elevated rates of nicotine and alcohol use are a particular risk for adolescents with CD and ADHD.
Design, methodology, and baseline data of the Personalized Addition Lenses Clinical Trial (PACT)

Background: The aim of this study was to describe the design, methods, and baseline characteristics of children enrolled in the Personalized Addition lenses Clinical Trial (PACT). PACT aims to test the myopia control efficacy of progressive addition lenses (PALs) with personalized addition values compared with standard (+2.00 D) addition PALs and single vision lenses (SVLs). Methods: PACT is a randomized, controlled, double-masked clinical trial. Two hundred eleven myopic Chinese children (7–12 years) were enrolled and randomized into 1 of the 3 following groups: personalized addition PALs; +2.00 addition PALs; and SVLs. Personalized addition values were determined based on the highest addition that satisfied Sheard criterion. Axial length and other biometric data were also recorded. Results: At baseline, no differences were found between the right and left eyes for any of the main parameters. The enrolled children were 9.7 ± 1.1 years’ old with cycloplegic autorefraction (right eye [OD]: −2.36 ± 0.64 D), near phoria (1.0 ± 5.0 prism diopter esophoria), lag of accommodation (1.40 ± 0.50 D) and axial length (OD: 24.58 ± 0.74 mm). The personalized addition values ranged from +0.75 to +3.00 (average ± SD: 2.19 ± 0.73 D). Conclusion: PACT is a clinical trial evaluating whether myopia progression in children can be slowed by wearing personalized addition PALs compared with fixed addition PALs and SVLs as measured by cycloplegic autorefraction and axial length. Baseline data were comparable with those of previous myopia control studies in children. Subjects will be followed up every 6 months for 2 years.
Computer-assisted anthropometry for outcome assessment of cleft lip.

Anthropometry and clinical examination best evaluate the morphology of repaired cleft lip and nose. An original, accurate, and practical image analysis of the lip and nose, which takes advantage of the mathematic, geometric, and organizational capabilities of public domain NIH-Image software (http://rsb.info.nih.gov/nih-image/), has been developed and tested over the past 6 years. A modified structured physical examination form that complements this analysis is under study. Accuracy of NIH-Image-based anthropometry was compared with direct measurements of 22 linear distances on the lip and nose. Twenty-five sets of direct measurements were taken, prospectively, on 15 children with repaired cleft lip over a 6-year period. The results were submitted to regression analysis. Then, relevant lip and nasal tip aesthetics were evaluated by the measuring capabilities of NIH-Image to create a quantitative assessment tool. For each episode, 15 possible faults were weighted, according to aesthetics and deformity, to provide an adverse score. The sum of the 5 lip scores, 10 nose scores, and combination gave respective grades. The analysis was modified to stratify congenital deformity to relate severity of disease to outcome. This analysis was applied to digitized images of 19 consecutive children, immediately prior to repair of complete unilateral cleft lip and nose, at the time of palate repair, and annually from the age of 3 to 6 years. There were 19 NIH-Image-based measurements of the congenital deformity and 35 measurements of surgical results; four children had three sets of records, eight had two sets, and seven had one set Descriptive statistics were applied. Following 556 paired direct and computer-assisted measurements, exceptional linear correlation was shown with a Pearson R coefficient of 0.96. The best correlation was lines within the plane of the camera lens, with the average difference ranging between 0.025 and 0.997 mm. Visual inspection of frontal and submental photographs of excellent, good, and poor results substantiates the ability of this analysis to quantify and grade a spectrum of relevant cleft lip and nasal anatomy. For these 19 patients, there was a broad range of performance scores, approximating a normal distribution. The mean of the NIH-Image-based analysis scores, 16.91, was a (very) good grade. A single standard deviation of 6.88 extended up into excellent and down to fair. The congenital analysis indicated a range of deformity. Comparing deformity with outcome, simple regression analysis had a coefficient of determination (R2) of 0.223, indicative of a weak positive relationship. An accurate and practical morphologic computer-assisted outcome assessment of repaired cleft lip and nasal deformity has been developed. There is a weak direct correlation between severity of deformity and outcome. Testing in multiple clinics is warranted.
Implementing IP Traceback in the Internet — An ISP Perspective

Denial-of-Service (DoS) attacks consume the resources of remote hosts and the network in terms of buffers, processing power, and connections, thus denying or degrading the Internet services to legitimate users. Managed security service (MSS) has been developed to provide better network performance in addition to protect customers from being attacked. IP traceback is one of the most important features incorporated in MSS. Probabilistic packet marking, a promising IP traceback scheme, has received much attention in the past couple of years, owing to its desirable properties. In this paper, we discuss the implementation issues of IP traceback technology from an ISP perspective. We introduce a practical marking scheme, in which the marking edge is a label representing a router instead of the router's IP address, and the marking probability is a function of the distance of the first trusted router on the attack path. To deal with spoofed marking, we also propose a hash-based scheme to validate the information in the marking field.