Miracle-dz/UniFAR-FTUs huggingface dataset:
Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside.

The recent release of the complete euchromatic genome sequence of Drosophila melanogaster offers a unique opportunity to explore the evolutionary history of transposable elements (TEs) within the genome of a higher eukaryote. In this report, we describe the annotation and phylogenetic comparison of 178 full-length long terminal repeat (LTR) retrotransposons from the sequenced component of the D. melanogaster genome. We report the characterization of 17 LTR retrotransposon families described previously and five newly discovered element families. Phylogenetically, these families can be divided into three distinct lineages that consist of members from the canonical Copia and Gypsy groups as well as a newly discovered third group containing BEL, mazi, and roo elements. Each family consists of members with average pairwise identities > or =99% at the nucleotide level, indicating they may be the products of recent transposition events. Consistent with the recent transposition hypothesis, we found that 70% (125/178) of the elements (across all families) have identical intra-element LTRs. Using the synonymous substitution rate that has been calculated previously for Drosophila (.016 substitutions per site per million years) and the intra-element LTR divergence calculated here, the average age of the remaining 30% (53/178) of the elements was found to be 137,000 +/-89,000 yr. Collectively, these results indicate that many full-length LTR retrotransposons present in the D. melanogaster genome have transposed well after this species diverged from its closest relative Drosophila simulans, 2.3 +/-. 3 million years ago.
Potential Use of Black Cotton Soil with additives as a Liner material to retain Zinc: Isotherm and Kinetic Studies

Land fill engineering plays an important role in management of hazardous wastes. To improve the performance of liners, additives like lime, cement and fly ash at low percentages were added to black cotton soil of Belgaum, Karnataka, India. This was used to study the leaching and sorption behaviour of zinc, isotherm and kinetic models have been applied to experimental data. Monolayer sorption capacity was obtained using Langmuir isotherm, which gave dependable results. Langmuir isotherm was found to be more suitable than Freundlich, Pseudo Second order gave better results than Pseudo First order, Elovich model and intraparticle diffusion model proved that adsorption, desorption and intraparticle diffusion operate concurrently during adsorbent and adsorbate interaction. It has been found that black cotton soil along with additives has good potential to attenuate zinc.
Comparison of Xilinx Virtex-II FPGA SEE sensitivities to protons and heavy ions

A comparison of heavy-ion and proton-induced single event effect sensitivities has been made using the Xilinx Virtex-II field programmable gate array (FPGA). Recently fabricated test samples are selected for observations of single event upset and single event functional interrupt. A complex relationship appears to exist between the heavy ion and proton sensitivities due to effects such as multiple-bit upsets and elastic nuclear scattering.
Declining Participation in Fraternity and Sorority Life: a Comparison of Perceptions of Greek-lettered Organizations Between Affiliated and Non-affiliated Students

This quantitative study was used to determine the perceptions that may have caused a decline in membership in fraternities and sororities and to examine active organization involvement between affiliated and unaffiliated students at a single higher education institution in northeast Texas. Eight perceptions were given regarding fraternity and sorority life and why students chose to remain unaffiliated with fraternities or sororities. The instrument used was a modified version of the Extracurricular Involvement Inventory, created by Winston and Massaro (1987) and was administered to participants online via Survey Monkey. There were 206 participants total: 55.3% were female, and 44.7% were male. Regarding ethnicities, 47.0% were African American, 37.5% were Caucasian, and 15.5% were Hispanic/Latino. Out of the participants, 20.9% were in their freshman or sophomore year, 23.8% were juniors, 33.5% were seniors, and 21.8% were graduate students. Participants’ ages ranged from 18 to 32, with a mean of 22.89 (SD = 2.81). The research questions were analyzed using two techniques: logistic regression for the first question and multiple regression for the second question. Findings for the first research question indicated that lack of values, lack of diversity, poor academic attitudes, and a requirement of too much time were primary reasons unaffiliated students chose not to join a fraternity or sorority. Findings for the second question indicated that Greek-affiliated students averaged higher involvement intensity scores when compared to unaffiliated students. Practical implications and future research are discussed.
Non-invasive transabdominal uterine electromyography correlates with the strength of intrauterine pressure and is predictive of labor and delivery

Objective: The study was conducted to investigate whether the strength of uterine contractions monitored invasively by intrauterine pressure catheter could be determined from transabdominal electromyography (EMG) and to estimate whether EMG is a better predictor of true labor compared to tocodynamometry (TOCO). Study design: Uterine EMG was recorded from the abdominal surface in laboring patients simultaneously monitored with an intrauterine pressure catheter (n = 13) or TOCO (n = 24). Three to five contractions per patient and corresponding electrical bursts were randomly selected and analyzed (integral of intrauterine pressure; integral, frequency, amplitude of contraction curve on TOCO; burst energy for EMG). The Mann–Whitney test, Spearman correlation and receiver operator characteristics (ROC) analysis were used as appropriate (significance was assumed at a value of p < 0.05). Results: EMG correlated strongly with intrauterine pressure (r = 0.764; p = 0.002). EMG burst energy levels were significantly higher in patients who delivered within 48 h compared to those who delivered later (median [25%/75%]: 96 640 [26 520–322 240] vs. 2960 [1560–10 240]; p < 0.001), whereas none of the TOCO parameters were different. In addition, burst energy levels were highly predictive of delivery within 48 h (AUC = 0.9531; p < 0.0001). Conclusion: EMG measurements correlated strongly with the strength of contractions and therefore may be a valuable alternative to invasive measurement of intrauterine pressure. Unlike TOCO, transabdominal uterine EMG can be used reliably to predict labor and delivery.
Age at menarche in Coimbra (Portugal) school girls: a note on the secular changes

The age at menarche and several menstrual symptoms were reported by 516 Portuguese school girls who took part in a cross-sectional anthropometric study in Coimbra, Portugal. The mean ages of menarche calculated using the recall method and also using probit analysis were 12.53 ± 1.27 and 12.03 ± 1.26 years, respectively. Parents' educational level, place of residence and size of the family did not have any significant effect on the mean age at menarche in this sample of adolescents. The order of birth was the only variable that indicated a significative effect: the firstborns reported a lower mean age at menarche (12.34 years) than the later borns (12.6 years). In this sample, 47% of the girls had a cycle length of ⩾̸ 29 days, 23.4% had irregular cycles, 59% reported that the duration of bleeding was 3-5 days and the majority, 49%, did not report any pain during the bleeding days. However, 14.3% and 24.45% reported severe and medium pain. The age at menarche has declined from 15.0 (girls born in 1880-1890) to 12.03 (girls born in 1970-1980) years in the Portuguese population. This decrease in age, and also the lack of influence of the family characteristics, appear as a result of the great improvements in the social and economic living conditions that occurred in Portugal, especially after the 1970s. These improvements are mainly related to better nutrition and better health care along with many other environmental factors.
A coding VKORC1 Asp36Tyr polymorphism predisposes to warfarin resistance.

CYP2C9 and VKORC1 genetic variants are associated with low and intermediate warfarin dose requirements, but markers of high doses are less well characterized. We analyzed the VKORC1 coding sequence and known CYP2C9 and VKORC1 polymorphisms in 15 selected warfarin-resistant (dose, 80 to 185 mg/wk) and 8 warfarin-sensitive patients (7 to 13 mg/wk) and 99 unselected controls (8 to 105 mg/wk). We identified a coding VKORC1 Asp36Tyr polymorphism in 7 of 15 resistant compared with 0 of 8 sensitive patients (P = .026) Carriers of Asp36Tyr in the control group (8 of 99) required significantly higher warfarin doses of 80.9 +/- 10.1 mg/wk compared with 42.7 +/- 7.5 mg/wk in noncarriers (F = 9.79, P = .002). Asp36Tyr was significantly associated with doses of more than 70 mg/wk (odds ratio, 13.0; 95% confidence limit, 1.3 to 124.2), while doses of 20 to 70 mg/wk were associated with Asp36Tyr (partial r(2) = . 11; P = . 004), CYP2C9*2 and *3 (r(2) = . 08; P = . 01), and VKORC1*2 and *3 markers (r(2) = . 05; P = . 05). All Asp36Tyr carriers also had VKORC1*1 tag-single nucleotide polymorphisms (tag-SNPs) indicating a new haplotype. Asp36Tyr was common in Jewish ethnic groups of Ethiopian (15%) and Ashkenazi (4%) origin. We suggest that Asp36Tyr is a new marker of the high end of the warfarin dosing range.
A morpho-phonological Past Tense processing as a clinical marker in SLI EFL learners

ABSTRACT The clinical marker in specific language impairment (SLI) population is the subject of considerable debate. SLI is the one of the frequently diagnosed atypical language phenomena found among early school-age children (McArthur et al., 2000; Spear-Swerling, 2006). For example, children with SLI have difficulty applying the Past Tense rule to verbs, even though they can accurately repeat phonologically similar forms of the words (Hoeffner & McClelland, 1993). In this study, I discuss the grammatical deficits in the SLI population by studying the generation of both ‘regular’ and ‘irregular’ English Past Tense forms and explain how the rates of the correct use of the ‘irregular’ versus ‘regular’ form may be considered as a clinical SLI marker. This study defines the differences in the grammatical sensitivity in the EFL learners and provides additional essential insight into SLI, in general, and its identification in the EFL learners, in particular.
Anti-Donor HLA Class I Antibodies: Pathways to Endothelial Cell Activation and Cell-Mediated Allograft Rejection

Background The development of donor-specific human leukocyte antigen (HLA) class I antibodies after organ transplantation is associated with subsequent acute and chronic rejection. The aim of this study was to examine the role of anti-HLA class I antibody in modulating endothelium–leukocyte interaction. Methods Human microvascular endothelial cells (HMEC-1) stimulated with HLA class I antibody (W6/32) or allospecific antibodies from sensitized patients (n=6) were examined for activation of transcription factor CREB by Western blotting. Up-regulation of endothelial adhesion molecules and chemokines was measured by flow cytometry and quantitative polymerase chain reaction, respectively. Leukocyte adhesion was evaluated by chemotaxis and in vitro flow-based assays. Results Treatment of HMEC-1 cells with HLA class I antibody resulted in the phosphorylation of CREB in protein kinase A–dependent pathway. Furthermore, there was a significant increase in the expression of cell surface VCAM-1 (Akt-dependent) and ICAM-1 in Akt-dependent and extracellular signal-regulated kinase–dependent manner (P<0.001). Additionally, exposure to W6/32 antibody induced significant expression of interleukin-6, CXCL8, CXCL10, and CCL5. Knockdown of CREB produced a reduction in W6/32-induced CXCL8 expression (P<0.001). Media from W6/32-treated endothelial cells induced a significant monocyte chemotaxis (P<0.001) and flow-based adhesion assay demonstrated an increase in monocyte adhesion to endothelial cells compared with the control group (P<0.001). Importantly, allospecific antibodies from sensitized patients also activated endothelial CREB and significantly up-regulated VCAM-1, ICAM-1, and CXCL8. Conclusion These findings suggest that donor-specific HLA class I antibodies directly activate endothelial cells leading to an increase in their potential to recruit and bind recipient leukocytes, thereby increasing the potential for allograft inflammation.
Optimization of Evening Insulin Dose in Patients Using the Short-Acting Insulin Analog Lispro

OBJECTIVE A three-way, crossover, open-label, randomized study was designed to compare the evening and night (1800–0800) glycemic control when the evening premeal lispro dose was reduced by 20% and the bedtime basal NPH dose increased by 25%, or when the basal NPH dose was moved to before dinner at 1800, compared with the control arm on standard premeal human regular insulin and pre-bedtime NPH insulin. RESEARCH DESIGN AND METHODS A total of 13 type 1 diabetic patients who use a premeal plus basal insulin regimen were studied on three separate days, with identical meals and snacks at the same times on each study day. On the control study day, patients received human regular insulin before dinner and NPH at bedtime in their usual doses. On another day, lispro was given before dinner with a dose reduction of 20%, and NPH at bedtime at 125% of usual dose. In the third regimen, the lispro and NPH were administered together in their usual dose before the evening meal by separate injections. The three regimens were tested in random order. RESULTS Postprandial (1800–2200) blood glucose concentrations were lower after reduced-dose lispro compared with human regular insulin (6.0 ± 0.3 [SEM] vs. 7.4 ± 0.3 mmol/1, P < 0.05). Nighttime (2400–0400) blood glucose concentrations were not different (8.6 ± 0.3 vs. 9.2 ± 0.3 mmol/1, NS), and prebreakfast concentrations were also unchanged (7.7 ± 0.9 vs. 8.7 ± 0.8 mmol/1) after lispro with increased-dose NPH compared with standard insulin. By contrast, both nighttime (10.0 ± 0.3 mmol/1, P < 0.05) and fasting glucose concentrations (10.8 ± 0.6 mmol/1, P < 0.05) were significantly higher with dinnertime usual-dose lispro plus dinnertime usual-dose NPH compared with standard human insulin. Hypoglycemia at night (blood glucose <3.0 mmol/1) did not differ between study days, but it was more frequent postprandially after dinner usual-dose lispro plus early NPH (2 vs. 7 patients, P = 0.062). CONCLUSIONS With lower mealtime and higher basal bedtime insulin doses, patients using insulin lispro may be able to gain an overall improvement in evening blood glucose control without deteriorated nighttime glucose levels. Earlier basal NPH dosage alone does not ameliorate the nighttime hyperglycemia of short-acting insulin analog regimens.
Further Stabilization of Earthworm Serine Protease by Chemical Modification and Immobilization

Earthworm serine protease is more stable and is less affected by organic solvents and detergent than other proteases. However, it is inactivated, probably by autolysis, at 60°C or above under alkaline conditions. Further stabilization was managed by chemical modification of the enzyme with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide and phenylglyoxal to protect the activity from the autolytic inactivation. Stabilization was possible also under acidic conditions, in which the stability of the enzyme was rather low, by immobilization with folded sheet mesoporous material. Thus, further stabilization of the enzyme has been achieved by chemical modification or immobilization.
Long-Term Effects of Valproic Acid on Reproductive Endocrine Functions in Turkish Women with Epilepsy

The long-term effects of valproic acid (VPA) on reproductive endocrine functions in women with epilepsy (WWE) were studied. Serum reproductive hormone concentrations, clinical findings and ovarian morphology were analyzed in 71 WWE who had been receiving antiepileptic drugs (AED) for a minimum of 2 years. Of the 71 WWE, polycystic ovarian syndrome (PCOS) (p = 0.011) and menstrual irregularities (p = 0.009) were found to be more prevalent in women receiving VPA treatment when compared to women on non-VPA treatment. There was no statistically significant dose or duration-related rise of risk for patients who developed PCOS and menstrual irregularities and those who were not on long-term VPA therapy. The lack of a duration-related reproductive dysfunction in this patient population may support the hypothesis of early occurring VPA-associated metabolic and endocrine changes.
Learner Agency, Dispositionality and the New Zealand Curriculum Key Competencies.

As more than just knowledge and skills, The New Zealand Curriculum (Ministry of Education, 2007) key competencies encompass dispositions for lifelong learning (OECD, 2005). A range of studies associate learner agency within the dispositions that are embedded in these key competencies (Carr, 2004; Hipkins, 2010; Hipkins & Boyd, 2011). Drawn from self-determination theory (OECD, 2009; Ryan & Deci, 2000), the competencies are strongly anchored in an essentialist frame-work. Interpreted this way, competencies can be likened to a virtual backpack that students carry about and draw from at will. A discursively constituted view of identity would suggest that this is not the case. Employing Davies’ (2010) conception of a subject-of-thought, where the subject is under erasure, the paper explores what agency as dispositionality can look like when it is performatively constituted in a competence-oriented curriculum (Ministry of Education, 2007). Rather being attributed static, essentialised identities, students are co-constituted in classroom discourses. The research has implications for how educators recognise moments when students agentically mobilise personal, social and discursive resources (Davies, 1990) in the classroom. This article presents an argument for a dynamic theory of agency that incorporates a rhizomatic view of learner participation and interrupts essentialist interpretations of dispositionality. It opens up possibilities for new conceptions of key competencies as performative discursive practices.
Real-Time Implementation of Fault-Tolerant Control Systems With Performance Optimization

In this paper, two online schemes for an integrated design of fault-tolerant control (FTC) systems with application to Tennessee Eastman (TE) benchmark are proposed. Based on the data-driven design of the proposed fault-tolerant architecture whose core is an observer/residual generator based realization of the Youla parameterization of all stabilization controllers, FTC is achieved by an adaptive residual generator for the online identification of the fault diagnosis relevant vectors, and an iterative optimization method for system performance enhancement. The performance and effectiveness of the proposed schemes are demonstrated through the TE benchmark model.
Digital Low-Pass Differentiation for Biological Signal Processing

Digital low-pass differentiation is often required in processing various biological or biomechanical data. However, both the nature of biological signals and the use of micro-or minicomputers in such applications imply the need for simple, low-order, and fast differentiation methods, rather than sophisticated high-order algorithms. Responding to this need, we investigate here the low-pass first- and second-order digital differentiation from both theoretical and practical points of view, in order to achieve good and simple algorithms. In contrast with most of the research works previously done in this field, whose main aim was to achieve better accuracy even in the cost of using quite high-order algorithms, we restrict ourselves in this study only to low orders, being interested not only in the accuracy achieved, but also in the simplicity of the algorithm. After discussing the theoretical considerations concerning our optimum low-pass differentiation filters, we present our simple low-order filters and show them to be not only very convenient for use, but also almost optimum.
Ability of a T-antigen transport-defective mutant of simian virus 40 to immortalize primary cells and to complement polyomavirus middle T in tumorigenesis

The oncogenic potential of polyomavirus in newborn rats could not be expressed by a genome encoding only the middle T antigen but required the presence of one of the other two viral early genes, small T or large T. The tumorigenicity defect could also be complemented by other viral or cellular genes that are known to be implicated in immortalization and establishment functions. The simian virus 40(cT)-3 mutant (R. E. Lanford and J. S. Butel, Cell 37:801-813, 1984), which fails to localize to the nucleus, has the capacity to complement polyomavirus middle T in tumorigenesis and to immortalize primary rat embryo fibroblasts when it was cotransfected in the presence of pSV2-neo. Our data suggested that under the conditions of DNA-mediated tumor induction and cotransfection with a dominant selection marker, the cellular alterations achieved by nonnuclear oncogenes such as polyomavirus small T and simian virus 40(cT)-3 were sufficient to complement polyomavirus middle T in transformation and tumorigenesis.
Identification of the PDZ3 Domain of the Adaptor Protein PDZK1 as a Second, Physiologically Functional Binding Site for the C Terminus of the High Density Lipoprotein Receptor Scavenger Receptor Class B Type I*

The normal expression, cell surface localization, and function of the murine high density lipoprotein receptor scavenger receptor class B type I (SR-BI) in hepatocytes in vivo, and thus normal lipoprotein metabolism, depend on its four PDZ domain (PDZ1–PDZ4) containing cytoplasmic adaptor protein PDZK1. Previous studies showed that the C terminus of SR-BI (“target peptide”) binds directly to PDZ1 and influences hepatic SR-BI protein expression. Unexpectedly an inactivating mutation in PDZ1 (Tyr20 → Ala) only partially, rather than completely, suppresses the ability of PDZK1 to control hepatic SR-BI. We used isothermal titration calorimetry to show that PDZ3, but not PDZ2 or PDZ4, can also bind the target peptide (Kd = 37.0 μm), albeit with ∼10-fold lower affinity than PDZ1. This binding is abrogated by a Tyr253 → Ala substitution. Comparison of the 1.5-Å resolution crystal structure of PDZ3 with its bound target peptide (505QEAKL509) to that of peptide-bound PDZ1 indicated fewer target peptide stabilizing atomic interactions (hydrogen bonds and hydrophobic interactions) in PDZ3. A double (Tyr20 → Ala (PDZ1) + Tyr253 → Ala (PDZ3)) substitution abrogated all target peptide binding to PDZK1. In vivo hepatic expression of a singly substituted (Tyr253 → Ala (PDZ3)) PDZK1 transgene (Tg) was able to correct all of the SR-BI-related defects in PDZK1 knock-out mice, whereas the doubly substituted [Tyr20 → Ala (PDZ1) + Tyr253 → Ala (PDZ3)]Tg was unable to correct these defects. Thus, we conclude that PDZK1-mediated control of hepatic SR-BI requires direct binding of the SR-BI C terminus to either the PDZ1 or PDZ3 domains, and that binding to both domains simultaneously is not required for PDZK1 control of hepatic SR-BI.