Miracle-dz/UniFAR-FTUs huggingface dataset:
Unleashing the Force of Cladistics? Metazoan Phylogenetics and Hypothesis Testing1

Abstract The accumulation of multiple phylogenetic hypotheses for the Metazoa invites an evaluation of current progress in the field. I discuss three case studies from the recent literature to assess how cladistic analyses of metazoan morphology have contributed to our understanding of animal evolution. The first case study on cleavage cross patterns examines whether a decade of unanimous character scoring across different cladistic studies can be considered a reliable indicator of accumulated wisdom. The two remaining case studies illustrate how the unique strength of cladistic analyses to arbitrate between competing hypotheses can be crippled when insufficient attention is directed towards the construction of the data matrix. The second case study discusses a recent morphological cladistic analysis aimed at providing insight into the evolution of larval ciliary bands (prototrochs) in the Spiralia, and the third case study evaluates how four subsequent morphological cladistic analyses have contributed to our understanding of the phylogenetic placement of a problematicum, the Myzostomida. I conclude that current phylogenetic analyses of the Metazoa have not fully exploited the power of cladistics to test available alternative hypotheses. If our goal is to generate genuine progress in understanding rather than stochastic variation of opinions through time, we have to shift our attention from using cladistics as an easy tool to generate “novel” hypotheses of metazoan relationships, towards employing cladistics more critically as an effective instrument to test the relative merit of available multiple alternative hypotheses.
Order-2 Stability Analysis of Particle Swarm Optimization

Several stability analyses and stable regions of particle swarm optimization (PSO) have been proposed before. The assumption of stagnation and different definitions of stability are adopted in these analyses. In this paper, the order-2 stability of PSO is analyzed based on a weak stagnation assumption. A new definition of stability is proposed and an order-2 stable region is obtained. Several existing stable analyses for canonical PSO are compared, especially their definitions of stability and the corresponding stable regions. It is shown that the classical stagnation assumption is too strict and not necessary. Moreover, among all these definitions of stability, it is shown that our definition requires the weakest conditions, and additional conditions bring no benefit. Finally, numerical experiments are reported to show that the obtained stable region is meaningful. A new parameter combination of PSO is also shown to be good, even better than some known best parameter combinations.
The association of recovery orientation and stigmatizing beliefs

Abstract Background: Although mental health advocates and providers have promoted both recovery-oriented care and the de-stigmatization of mental illness, no studies have examined the interrelation of these two specific constructs. Aims: This study aimed to evaluate this association, with the hypothesis that stronger perception of programmatic recovery orientation would be associated with less stigmatizing beliefs towards mental illness. Method: Veterans (N = 122) and mental health clinicians (N = 98) at a large Veterans Affairs Medical Center completed an assessment of recovery orientation and a measure of beliefs about mental illness. Results: Stronger endorsement of programmatic recovery orientation was associated with less stigmatizing attitudes in both groups. Each of the five factors on the recovery measure was significantly and negatively associated with each of the four factors on the stigma measure. Conclusions: Perspectives of recovery orientation and stigma are significantly, but negatively, associated. Future research should investigate the direction of causality behind these observed relationships, as this will provide the opportunity to identify potential interventions to increase recovery-oriented mental health care and reduce stigmatization.
Assessment of the cellular response to the induced expression of defensin sense and antisense cDNA in acute promyelocytic leukemia cell lines

Defensins are 20-30 amino acid-long, cystine- and arginine-rich peptides that constitute more than 5% of the total cellular proteins in mature granulocytes and at least 30% of proteins in primary granules. Human defensins were reported to have antimicrobial, antifungal, antiviral and tumor lysis activities. Defensin mRNA was isolated using the differential display technique from the well-characterized all-trans retinoic acid (ATRA)-responsive acute promyelocytic leukemia cell line, NB4. The differential display analysis showed an up-regulation of defensin mRNA in NB4 cells after treatment with 10(-7) M ATRA for 24 h. This expression was not seen in an NB4:R2 cell line, an ATRA-resistant subclone of NB4 cells. In order to investigate further the effects of this gene on our cellular model, we virally infected our cells with full-length defensin cDNA in the sense and antisense directions. Sense defensin induced cell growth arrest and cell death in both cell lines. While NB4 cells died within 48-73 h, NB4:R2 cells survived for 96 h before dying in culture. Phenotypic analysis showed high expression of Annexin V in sense-infected cells compared with antisense and uninfected cells in both cell lines. There was not a significant increase in CD11b expression in any of the 2 cell lines used. No cellular response was encountered in antisense-infected cells. Our data suggest that defensin is not only a reliable marker for granulocytic differentiation, but can also be considered a candidate target for molecular therapy in acute promyelocytic leukemia.
I NCREASING I NDUSTRIAL P RODUCTIVITY BY E MPLOYING A S MART S PEECH -B ASED Q UESTION A NSWERING A SSISTANT

: This paper proposes a system design for a question-answering assistant, aiming to increase the productivity in industrial environments. The system is characterized by the fact that its components and domain speciﬁc knowledge are embedded on a given hardware platform locally. The effects of introducing a prototype-assistant on the productivity and the perceived workload are explored empirically by conducting experiments designed for this purpose. As a result, users were able to answer the given questions faster when using the prototype than when searching manually. Moreover, after employing the prototype, users reported their task to be less demanding, with a positive effect on the human-machine interaction.
Relationship of aerobic and anaerobic parameters with 400 m front crawl swimming performance

The aims of the present study were to investigate the relationship of aerobic and anaerobic parameters with 400 m performance, and establish which variable better explains long distance performance in swimming. Twenty-two swimmers (19.1±1.5 years, height 173.9±10.0 cm, body mass 71.2±10.2 kg; 76.6±5.3% of 400 m world record) underwent a lactate minimum test to determine lactate minimum speed (LMS) (i.e., aerobic capacity index). Moreover, the swimmers performed a 400 m maximal effort to determine mean speed (S400m), peak oxygen uptake (V.O2PEAK) and total anaerobic contribution (CANA). The CANA was assumed as the sum of alactic and lactic contributions. Physiological parameters of 400 m were determined using the backward extrapolation technique (V.O2PEAK and alactic contributions of CANA) and blood lactate concentration analysis (lactic anaerobic contributions of CANA). The Pearson correlation test and backward multiple regression analysis were used to verify the possible correlations between the physiological indices (predictor factors) and S400m (independent variable) (p < 0.05). Values are presented as mean ± standard deviation. Significant correlations were observed between S400m (1.4±0.1 m·s-1) and LMS (1.3±0.1 m·s-1; r = 0.80), V.O2PEAK (4.5±3.9 L·min-1; r = 0.72) and CANA (4.7±1.5 L·O2; r= 0.44). The best model constructed using multiple regression analysis demonstrated that LMS and V.O2PEAK explained 85% of the 400 m performance variance. When backward multiple regression analysis was performed, CANA lost significance. Thus, the results demonstrated that both aerobic parameters (capacity and power) can be used to predict 400 m swimming performance.
Design of a compact 77-GHz CMOS on-chip bandpass filter using U-type dual-spiral resonators

A first reported ultra-comapct 77-GHz CMOS on-chip bandpass filter (BPF) fabricated in TSMC 0.18-µm standard CMOS process is presented. The U-type dual-spiral resonators are utilized to reduce the size of the filter. The extra transmission zero is generated by the tapped-line input/output feed structure. The transmission zero at the lower stopband is located at 57 GHz. The selectivity of the proposed filter is much enhanced. The ultra-compact chip size of the proposed filter is 0.17 × 0.405 mm2. The good agreement between simulation and measurement is obtained.
Changes in polypeptide composition of Synechocystis sp. strain 6308 phycobilisomes induced by nitrogen starvation

Phycobilisomes isolated from actively growing Synechocystis sp. strain 6308 (ATCC 27150) consist of 12 polypeptides ranging in molecular mass from 11.5 to 95 kilodaltons. The phycobilisome anchor and linker polypeptides are glycosylated. Nitrogen starvation causes the progressive loss of phycocyanin and allophycocyanin subunits with molecular masses between 16 and 20 kilodaltons and of two linker polypeptides with molecular masses of 27 and 33 kilodaltons. Nitrogen starvation also leads to enrichment of four additional polypeptides with molecular masses of 46, 53, 57, and 61 kilodaltons and a transient enrichment of 35- and 41-kilodalton polypeptides in isolated phycobilisomes. The 57-kilodalton additional polypeptide was identified by immunoblotting as the large subunit of ribulosebisphosphate carboxylase/oxygenase. Proteins with the same molecular weights as the additional polypeptides were also coisolated with the 12 phycobilisome polypeptides in the supernatant of nitrogen-replete Synechocystis thylakoid membranes extracted in high-ionic-strength buffer and washed with deionized water. These observations suggest that the additional polypeptides in phycobilisomes from nitrogen-starved cells may be soluble or loosely bound membrane proteins which associate with phycobilisomes. The composition and degree of association of phycobilisomes with soluble and adjacent membrane polypeptides appear to be highly dynamic and specifically regulated by nitrogen availability. Possible mechanisms for variation in the strength of association between phycobilisomes and other polypeptides are suggested.
Alveolar Macrophage Recruitment and Activation by Chronic Second Hand Smoke Exposure in Mice

Approximately 15% of cases of COPD occur in non-smokers. Among the potential risk factors for COPD in non-smokers is second-hand smoke (SHS) exposure. However, the Surgeon General reported in 2006 that the evidence linking second hand smoke and COPD is insufficient to infer a causal relationship, largely because current evidence does not establish a biological link. The goal of this study was to determine whether SHS exposure can induce alveolar macrophage recruitment and expression of activation markers that we have previously demonstrated in human smokers and in mouse models of emphysema. To achieve these goals, we studied mice exposed to an ambient mixture of predominantly [89%] sidestream smoke at increasing doses over 3 months. We found that second hand smoke exposure induced a dose-dependent increase in alveolar macrophage recruitment (mean ± sd; 224,511 ± 52,330 vs 166,152 ± 47,989 macrophages/ml of bronchoalveolar lavage in smoke-exposed vs air-exposed controls at 3 months, p = 0.003). We also found increased expression of several markers of alveolar macrophage activation (PLA2g7, dkfzp434l142, Trem-2, and pirin, all p < 0.01 at 3 months) and increased lavage levels of two inflammatory mediators associated with COPD (CCL2 [MCP-1], 58 ± 12 vs. 43 ± 22 pg/ml, p = 0.03; and TNFα, 138 ± 43 vs 88 ± 78 pg/ml, p = 0.04 at 3 months). These findings indicate that second smoke exposure can cause macrophage recruitment and activation, providing a biological link between second-hand smoke exposure and the development of inflammatory processes linked to COPD.
South Asian dietary patterns and their association with risk factors for the metabolic syndrome.

BACKGROUND Certain dietary patterns have been associated with higher risk of noncommunicable diseases, with South Asians identified as a high-risk group. The present study aimed to identify the association between dietary patterns and the metabolic syndrome (MS) in South Asians living in the UK. METHODS Dietary patterns were derived by principal component analysis from 15 different food groups using an ethnic-specific food frequency questionnaire. MS risk factors, including obesity and hypertension, were measured, whereas existing conditions of dyslipidaemia and hyperglycaemia were self-reported. Participants (n = 100) were divided into quartiles based on dietary factor scores and the link between dietary patterns and risk factors was investigated. RESULTS Three different patterns were derived, which together explained 46% of the total diet variation; eastern pattern, mixed pattern and western pattern. An inverse correlation was found between the eastern pattern and education P = 0.05). A direct correlation was found between the western pattern and physical activity (P = 0.05) and the overall risk of MS (P = 0.05). Body composition was altered as residence time in the UK increased, with a reduction in muscle mass (29-26%) and an increase in body fat (31-37%). Diagnosis criteria for MS were found in 20% of the participants. CONCLUSIONS Dietary acculturation, including a reduction in vegetarianism, an increased intake of caffeinated drinks and altered meal patterns, may be associated with the higher prevalence of MS in migrant South Asians in the UK.
Comparing Children’s and Caseworkers’ Reports of Physical Violence

In cases of suspected child maltreatment, the caseworkers’ evaluations of the harm and risk to the child are vital in determining if children are being abused and ultimately whether services are provided to the family. These evaluations are dependent on information caseworkers are able to uncover during their investigation, but may not reflect the experiences of the child. Using data from the National Survey of Child and Adolescent Well-Being (NSCAW-I), this study first compares how consistent children’s claims of physical victimization are with caseworkers’ assessments of harm, severity of risk, and whether there is physical abuse occurring. Second, we examine whether any discrepancies are influenced by the demographic characteristics of the child. Based on cross-tabulations, mean tests of difference, and one-way ANOVA, we find a high degree of overlap in children’s reports of violence with caseworkers’ reports of harm, the potential for risk, and the presence of physical abuse. However, there are also important differences. Among children who reported acts of physical violence occurred “lots of times,” 23% of the cases were viewed by the caseworker as causing “no harm” to the child and over 60% were not regarded as physical abuse. The children’s age and sex are both significant predictors of discrepancies, with more discrepancies between caseworkers and young children or teens as well as boys. Implications of this study are that additional training is needed to help caseworkers build rapport with the children. We also suggest that Child Protective Services (CPS) should implement alternative ways for children to report their experiences other than face-to-face interviews with caseworkers.
Reconstruction of body cavity volume in terrestrial tetrapods

Although it is generally assumed that herbivores have more voluminous body cavities due to larger digestive tracts required for the digestion of plant fiber, this concept has not been addressed quantitatively. We estimated the volume of the torso in 126 terrestrial tetrapods (synapsids including basal synapsids and mammals, and diapsids including birds, non‐avian dinosaurs and reptiles) classified as either herbivore or carnivore in digital models of mounted skeletons, using the convex hull method. The difference in relative torso volume between diet types was significant in mammals, where relative torso volumes of herbivores were about twice as large as that of carnivores, supporting the general hypothesis. However, this effect was not evident in diapsids. This may either reflect the difficulty to reliably reconstruct mounted skeletons in non‐avian dinosaurs, or a fundamental difference in the bauplan of different groups of tetrapods, for example due to differences in respiratory anatomy. Evidently, the condition in mammals should not be automatically assumed in other, including more basal, tetrapod lineages. In both synapsids and diapsids, large animals showed a high degree of divergence with respect to the proportion of their convex hull directly supported by bone, with animals like elephants or Triceratops having a low proportion, and animals such as rhinoceros having a high proportion of bony support. The relevance of this difference remains to be further investigated.
Multiple frequency compositing of spatially coincident GPR data sets

The compositing of spatially coincident GPR data sets acquired over a range of different antenna frequencies is a possible method for expanding the spectral bandwidth. A modelling study using the Berlage wavelet to represent the GPR source signature shows that the best results are obtained by applying an appropriate shift and weighting to the individual frequency components before compositing. It was also determined that application of only the weighting procedure significantly enhanced the composite signal. Compositing was performed on two spatially coincident multiple frequency data sets to examine its implementation with actual field data. A pre-compositing linear mute effectively suppressed the lower frequency direct wave interference with the very shallow reflections in higher frequency profiles. The best compositing results were obtained by using an optimal spectral whitening procedure to estimate the component weightings.
Longitudinal biobanks-based study on the joint effects of infections, nutrition and hormones on risk of prostate cancer

Abstract Background To evaluate the individual and combined effects of enterolactone, vitamin D, free testosterone, Chlamydia trachomatis and HPV-18 on the risk of prostate cancer in a large population-based biochemical material that combined three Nordic serum sample banks. Material and methods A joint cohort of 209 000 healthy men was followed using cancer registry linkages. From this cohort altogether 699 incident cases of prostate cancer were identified. Four controls were selected by incidence density sampling and matching for country, age and date of the blood sampling. Complete data for all investigated exposures was available for 483 eligible cases and 1055 eligible controls. Multivariate regression analyses were performed to investigate the solitary and combined effects. Results The solitary effects were small. Significantly increased risk [rate ratio 1.6 (95% CI 1.0–2.5)] was found in those seronegative for C. trachomatis infection. The joint effect in risk levels of enterolactone and vitamin D was antagonistic [observed rate ratio (RR) 1.4 (1.0–2.1), expected RR 2.0 (1.0–4.1)] as well as that of HPV-18 and C. trachomatis [observed RR 1.9 (0.8–4.5), expected RR 9.9 (1.1–87.0)]. Conclusion A large follow-up study combining data from several previously investigated exposures to investigate joint effects found no evidence that exposure to two risk factors would increase the risk of prostate cancer from that expected on basis of exposure to one risk factor. If anything, the results were consistent with antagonistic interactions.
Demonstration of Conformational Changes Associated with Activation of the Maltose Transport Complex*

In Escherichia coli, interaction of a periplasmic maltose-binding protein with a membrane-associated ATP-binding cassette transporter stimulates ATP hydrolysis, resulting in translocation of maltose into the cell. The maltose transporter contains two transmembrane subunits, MalF and MalG, and two copies of a nucleotide-hydrolyzing subunit, MalK. Mutant transport complexes that function in the absence of binding protein are thought to be stabilized in an ATPase-active conformation. To probe the conformation of the nucleotide-binding site and to gain an understanding of the nature of the conformational changes that lead to activation, cysteine 40 within the Walker A motif of the MalK subunit was modified by the fluorophore 2-(4′-maleimidoanilino)naphthalene-6-sulfonic acid. Fluorescence differences indicated that residues involved in nucleotide binding were less accessible to aqueous solvent in the binding protein independent transporter than in the wild-type transporter. Similar differences in fluorescence were seen when a vanadate-trapped transition state conformation was compared with the ground state in the wild-type transporter. Our results and recent crystal structures are consistent with a model in which activation of ATPase activity is associated with conformational changes that bring the two MalK subunits closer together, completing the nucleotide-binding sites and burying ATP in the interface.
Expression Profiling of Genes Involved in Collagen Turnover in Tendons from Cerebral Palsy Patients

Cerebral palsy (CP) is a nonprogressive central nervous system lesion clinically characterized by impairment of voluntary movement related to spasticity, time of activation, and strength of scheletal muscle. Altered muscular control may act on tendon structure and influence extracellular matrix homeostasis, in particular, collagen. The effect of spasticity on collagen turnover in CP patients’ tendons has not been described previously. We studied collagen turnover related genes in the gracilis and semitendinosus tendons of diplegic (n = 6) and quadriplegic (n = 15) patients, compared to normal subjects (n = 7). In particular, using real time RT-PCR, we analyzed the mRNA levels of the major extracellular matrix (ECM) components collagen type I (COL-I, alpha 2 chain COL1A2), the matrix metalloproteinase-1 (MMP-1) and the tissue inhibitor of MMP (TIMP-1), the enzyme responsible for collagen maturation lysyl hydroxylase 2b (LH2b), of the matricellular protein involved ECM remodelling (secreted protein acidic and rich in cysteine, SPARC), and the transforming growth factor-β1 (TGF-β1), a multipotent cytokine involved in collagen turnover. Our results show that gene expression profiles are quite different in CP samples compared to normal ones. In fact, spasticity induces relevant modifications of tendons at the molecular level, which modify their phenotypes to respond to the higher mechanical loading and increased functional demands. Interestingly, hypertonic quadriplegic subjects displayed the highest mRNA levels of COL1A2, LH2b, TGF-β1, and SPARC, suggesting that their tendons undergo higher mechanical loading stimulation.