Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of alignment in morphology and prosody : the case of Polish

This dissertation investigates the role of alignment in morphology and phonology and its implications for the theory of Generalised Alignment (McCarthy & Prince 1993) via a close examination of Polish data. An issue of great theoretical interest is the asymmetry between Left and Right Alignment. Left Alignment enjoys a privileged treatment in prosody and morphology. In prosody, LEFT alignment is obeyed even in languages with right oriented primary stress: left alignment is crucial in the assignment of secondary stress. A similar asymmetry applies to ANCHORING. A detailed study of truncation reveals that Left Anchoring is preferred over Right Anchoring. The source of this asymmetry is sought in left-to-right processing (Hay 2002). I argue, against Nelson (2003), that in spite of this preference, RIGHT Anchoring cannot be replaced by other Anchor constraints, such as Anchoring to head foot. Another issue addressed in this dissertation is the type of material that can be aligned. I concentrate on segmental feature spreading (palatalisation and voicing) across morpheme boundaries. Palatalisation does not spread across prefix/stem boundaries and obeys Align (Feature, Stem). Voicing is immune to Alignment and spreads across the whole obstruent cluster. This asymmetry is grounded in articulation. Spreading of palatalisation involves an additional tongue movement towards the hard palate. De/voicing involves a complete readjustment of the glottis, which is more difficult to control than the palatalising tongue movement. Lastly, I show that primary and secondary stresses can be sensitive to different prosodic domains in a single grammar. In Polish, primary stress aligns with the Morphosyntactic Word, while secondary stress aligns with the Prosodic Word. Further, I investigate the mode of violation of the alignment constraints and I argue, contra (McCarthy 2003) that violation of constraints cannot be categorical.
Chronic pelvic pain in women of reproductive and post‐reproductive age: a population‐based study

Epidemiological studies on chronic pelvic pain (CPP) have focused on women of reproductive age. We aimed to determine the prevalence of chronic pelvic pain (CPP) in adult women and the differences in associated factors among women of reproductive age and older women. In addition, to determine whether distinct subgroups existed among CPP cases.
The ritual stance and the precaution system: the role of goal-demotion and opacity in ritual and everyday actions

ABSTRACT Rituals tend to be both causally opaque and goal demoted, yet these two qualities are rarely dissociated in the literature. Here we manipulate both factors and demonstrate their unique influence on ritual cognition. In a 2 × 3 (action type x goal information) between subjects design 484 US adults viewed causally opaque (ritual) or causally transparent (ordinary) actions performed on identical objects. They were provided with no goal information, positive goal information (“Blessing”) or negative goal information (“Cursing”). Neither causal opacity nor goal information influenced perceptions of physical change/causation. In contrast, causal opacity increased attributions of “specialness,” whereas goal information did not. Finally, goal information interacted with action type on measures of preference, such that ordinary actions are influenced by both “blessings” and “curses,” but ritual actions are only influenced by “curses. ” These findings are interpreted in light of the Ritual Stance, and the cognitive bases of the effects are described with reference to Boyer and Liénard's hazard-precaution theory of ritualized behavior. The combined value of these two theories is discussed, and extended to a causal model of developmental ritual “calibration. ”
Study of the relationship between mononuclear inflammatory infiltrate and Ki-67 and basement membrane and extracellular matrix protein expression in radicular cysts.

AIM To evaluate the relationship between mononuclear inflammatory infiltrate and the expression of a proliferative immunomarker (Ki-67) as well as to evaluate basement membrane and extracellular matrix proteins (laminin and collagen type IV) in radicular cysts and dentigerous cysts (DC). METHODOLOGY Immunohistochemical analyses were performed in heavily inflamed radicular cysts (HIRC), slightly inflamed radicular cysts (SIRC) and DC (n = 20) using Ki-67 (Dako(®) , 1 : 50), anticollagen type IV (DBS(®) , 1 : 40) and antilaminin (DBS(®) , 1 : 20). The data were analysed using anova/Tukey's test (Ki-67) and Kruskal-Wallis/Dunn's test (collagen type IV and laminin) (P < 0.05). RESULTS The immunoexpression of Ki-67 was significantly greater in the SIRC group compared with the HIRC and DC (P = 0.0040). Likewise, the immunoexpression of collagen type IV in the basement membrane of the SIRC group was significantly more continuous (P = 0.0475) than in the HIRC group. DC had significantly less collagen type IV in extracellular matrix immunoexpression than HIRC and SIRC (P = 0.0246). Laminin was absent in the basement membrane in the SIRC and DC groups, and the extracellular matrix of the HIRC was weak and punctate. CONCLUSION The presence of inflammatory factors in the radicular cyst wall modified the expression of proliferation factors in the epithelial lining and the expression of collagen type IV and laminin in the basement membrane, but did not modify extracellular matrix behaviour in radicular cysts.
Benthic iron cycling in a high‐oxygen environment: Implications for interpreting the Archean sedimentary iron isotope record

The most notable trend in the sedimentary iron isotope record is a shift at the end of the Archean from highly variable δ56Fe values with large negative excursions to less variable δ56Fe values with more limited negative values. The mechanistic explanation behind this trend has been extensively debated, with two main competing hypotheses: (i) a shift in marine redox conditions and the transition to quantitative iron oxidation; and (ii) a decrease in the signature of microbial iron reduction in the sedimentary record because of increased bacterial sulfate reduction (BSR). Here, we provide new insights into this debate and attempt to assess these two hypotheses by analyzing the iron isotope composition of siderite concretions from the Carboniferous Mazon Creek fossil site. These concretions precipitated in an environment with water column oxygenation, extensive sediment pile dissimilatory iron reduction (DIR) but limited bacterial sulfate reduction (BSR). Most of the concretions have slightly positive iron isotope values, with a mean of 0.15‰ and limited iron isotope variability compared to the Archean sedimentary record. This limited variability in an environment with high DIR and low BSR suggests that these conditions alone are insufficient to explain Archean iron isotope compositions. Therefore, these results support the idea that the unusually variable and negative iron isotope values in the Archean are due to dissimilatory iron reduction (DIR) coupled with extensive water column iron cycling.
Protective effects of casein-derived peptide VLPVPQK against hydrogen peroxide–induced dysfunction and cellular oxidative damage in rat osteoblastic cells

Oxidative stress inhibits osteoblast differentiation and function that lead to the development of osteoporosis. Casein-derived peptide VLPVPQK (PEP), a potent antioxidant, was isolated from β-casein of buffalo milk. We used an in vitro oxidative stress model induced by hydrogen peroxide (H2O2) in rat osteoblastic cells to investigate the protective effects of PEP against H2O2-induced dysfunction and oxidative damage. Cells were pretreated with PEP (50–200 ng/mL) for 2, 7 or 21 days followed by 0.3 mM H2O2 treatment for 24 h and then markers of osteogenic development, oxidative damage and apoptosis were examined. PEP significantly increased the viability and differentiation markers of osteoblast cells such as alkaline phosphatase and calcium mineralization. Moreover, PEP suppressed the production of reactive oxygen species (ROS), lipid peroxidation and ameliorated H2O2-induced reduction in glutathione, superoxide dismutase and catalase activities. In addition, PEP partially inhibited caspase-9 and-3 activities and reduced propidium iodide–positive cells. Altogether, our results demonstrated that PEP could protect rat osteoblast against H2O2-induced dysfunction and oxidative damage by reduction of ROS production, lipid peroxidation and increased antioxidant enzyme activities. Thus, our data suggest that PEP might be a valuable protective agent against oxidative stress–related diseases such as osteoporosis.
Prognostic Significance of Diffuse Large B-Cell Lymphoma Cell of Origin Determined by Digital Gene Expression in Formalin-Fixed Paraffin-Embedded Tissue Biopsies.

PURPOSE To evaluate the prognostic impact of cell-of-origin (COO) subgroups, assigned using the recently described gene expression-based Lymph2Cx assay in comparison with International Prognostic Index (IPI) score and MYC/BCL2 coexpression status (dual expressers). PATIENTS AND METHODS Reproducibility of COO assignment using the Lymph2Cx assay was tested employing repeated sampling within tumor biopsies and changes in reagent lots. The assay was then applied to pretreatment formalin-fixed paraffin-embedded tissue (FFPET) biopsies from 344 patients with de novo diffuse large B-cell lymphoma (DLBCL) uniformly treated with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) at the British Columbia Cancer Agency. MYC and BCL2 protein expression was assessed using immunohistochemistry on tissue microarrays. RESULTS The Lymph2Cx assay provided concordant COO calls in 96% of 49 repeatedly sampled tumor biopsies and in 100% of 83 FFPET biopsies tested across reagent lots. Critically, no frank misclassification (activated B-cell-like DLBCL to germinal center B-cell-like DLBCL or vice versa) was observed. Patients with activated B-cell-like DLBCL had significantly inferior outcomes compared with patients with germinal center B-cell-like DLBCL (log-rank P < .001 for time to progression, progression-free survival, disease-specific survival, and overall survival). In pairwise multivariable analyses, COO was associated with outcomes independent of IPI score and MYC/BCL2 immunohistochemistry. The prognostic significance of COO was particularly evident in patients with intermediate IPI scores and the non-MYC-positive/BCL2-positive subgroup (log-rank P < .001 for time to progression). CONCLUSION Assignment of DLBCL COO by the Lymph2Cx assay using FFPET biopsies identifies patient groups with significantly different outcomes after R-CHOP, independent of IPI score and MYC/BCL2 dual expression.
The Impact of Palliative Care Consultation in the ICU on Length of Stay

Introduction: The intensive care unit (ICU) consumes 20% of hospital expenditures and 1% of gross domestic product. Many strategies have been attempted to reduce ICU costs. A systematic review was conducted to evaluate the effect of palliative care (PC) consultations in the ICU on length of stay (LOS) and costs. Methods: A literature search was performed using PubMed, MEDLINE, EMBASE, and the Cochrane Library. Randomized controlled trials (RCTs), prospective, and retrospective cohort studies looking at PC consultations in adult ICUs published between January 2000 and February 2016 were selected. Independent reviewers assessed the eligibility of studies, extracted data on ICU, hospital LOS, and mortality, and rated each study’s quality. The cost was derived from an existing model in the literature; the primary outcome was ICU LOS and the secondary outcomes were direct variable costs, mortality, and hospital LOS. Results: We reviewed 814 abstracts, but only 8 studies met inclusion criteria and were included. The patients with a PC consultation in the ICU, when compared to those who did not, showed a trend toward reduced LOS. This reduction was statistically significant in the higher quality studies. Mortality was similar in both groups. Palliative care consultations also lead to a reduction in costs in 5 of the 8 eligible trials. On average, ICU costs were USD7533 and USD6406 (control vs PC, P < .05) and hospital direct variable costs were USD9518 and USD8971 (P < .05) per admission. Due to interstudy heterogeneity, all outcomes were described narratively. Conclusion: This review demonstrates a trend that PC consultations reduce LOS and costs without impacting mortality. However, due to the small sample sizes and varying degrees of quality of evidence, many questions remain. A large multicenter RCT and formal economic evaluation would be needed for more definitive results.
Molecular combing reveals complex 4q35 rearrangements in Facioscapulohumeral dystrophy

Facioscapulohumeral dystrophy (FSHD), one of the most common hereditary neuromuscular disorders, is associated with a complex combination of genetic variations at the subtelomeric 4q35 locus. As molecular diagnosis relying on Southern blot (SB) might be challenging in some cases, molecular combing (MC) was recently developed as an additional technique for FSHD diagnosis and exploration of the genomic organization of the 4q35 and 10q26 regions. In complement to the usual SB, we applied MC in a large cohort of 586 individuals with clinical FSHD. In 332 subjects, the two 4q alleles were normal in size, allowing exclusion of FSHD1 while we confirmed FSHD1 in 230 patients. In 14 patients from 10 families, we identified a recurrent complex heterozygous rearrangement at 4q35 consisting of a duplication of the D4Z4 array and a 4qA haplotype, irresolvable by the SB technique. In five families, we further identified variations in the SMCHD1 gene. Impact of the different mutations was tested using a minigene assay and we analyzed DNA methylation after sodium bisulfite modification and NGS sequencing. We discuss the involvement of this rearrangement in FSHD since all mutations in SMCHD1 are not associated with D4Z4 hypomethylation and do not always segregate with the disease.
Bioactive injectable aggregates with nanofibrous microspheres and human dental pulp stem cells: A translational strategy in dental endodontics

Regeneration of the pulp–dentin complex with stem cells is a potential alternative to conventional root canal treatments. Human dental pulp stem cells (hDPSCs) have been extensively studied because of their ability to proliferate and differentiate into mineralized dental and non‐dental tissues. Here we combined hDPSCs with two types of injectable poly‐l‐lactic acid (PLLA) microsphere with a nanofibrous or smooth surface to form bioactive injectable aggregates, and examined their ability to promote pulp regeneration in the root canal in an in vivo model. We investigated the biocompatibility, biosafety and odontogenic potential of fibrous (F‐BIM) and smooth bioactive injectable microspheres (S‐BIM) in vitro and in vivo. Our results demonstrated that PLLA microspheres and hDPSCs were able to form bioactive injectable aggregates that promoted dentin regeneration in both in vitro and in vivo models. Our results suggest that F‐BIM and S‐BIM may induce dentinogenesis upon in vivo grafting, and propose that the potential usefulness of the microsphere–hDPSC aggregates described here should be evaluated in clinical settings. Copyright © 2017 John Wiley & Sons, Ltd.
E-Reading and the Christian Bible

The Christian Bible is now available in thousands of digital forms, re-imagined for electronic reading on mobile, tablet and desktop screens. This article introduces findings from an online survey of digital Bible users, analysing their demographics, reading practices, motivations and experiences. Survey responses are analysed in conversation with recent debates among Christian commentators and broader arguments in the study of e-reading in education and other contexts. Religious e-reading shows some distinctive and unexpected features, in comparison with reading in other contexts, and this article proposes some initial hypotheses about the impact of digital media on sacred text.
Protective role of R381Q (rs11209026) polymorphism in IL-23R gene in immune-mediated diseases: A comprehensive review

Abstract Interleukin-23 (IL-23) is a regulator of cellular immune responses involved in controlling infection and autoimmune diseases. Strong evidence has shown that IL-23 plays a role in the maintenance of immune responses by influencing the proliferation and survival of IL-17-producing T-helper (TH)-17 cells. The critical role of the IL-23/TH17 axis in immune-mediated diseases has emerged from different studies. It has also been seen that polymorphisms in the IL-23 receptor (IL-23R) gene might influence IL-23 responses. Interestingly, a functional single nucleotide polymorphism (SNP) in the IL-23 receptor gene (IL-23R; rs11209026, 1142 G wild-type A reduced function, Arg381Gln, R381Q) seems to confer a measure of protection against development of inflammatory bowel disease (IBD; Crohn’s disease, ulcerative colitis), ankylosing spondylitis, rheumatoid arthritis, psoriasis, thyroiditis, recurrent spontaneous abortion and asthma, suggesting that a perturbation in the IL-23 signaling pathway is likely to be relevant to the pathophysiology of these diseases. The aim of this review was to provide an evaluation of what is currently known about the protective role of R381Q variant in IL-23R gene in immune-based diseases.
Reduced mRNA expression of nucleotide excision repair genes in lymphocytes and risk of squamous cell carcinoma of the head and neck

Nucleotide excision repair (NER) plays a critical role in the development of smoking-related cancers. We hypothesize that mRNA expression levels of NER genes are associated with risk of the squamous cell carcinoma of head and neck (SCCHN). To test this hypothesis, we conducted a case-control study of 260 SCCHN patients and 246 cancer-free controls by measuring the mRNA expression levels of eight core NER genes in cultured peripheral lymphocytes. Compared with the controls, cases had statistically significantly lower expression levels of DDB1 and ERCC3 (P = 0.015 and 0.041, respectively). Because DDB1 and ERCC3 expression levels were highly correlated, we used DDB1 for further multivariate analyses and modeling. After dividing the subjects by controls' quartiles of expression levels, we found an association between an increased risk of SCCHN and low DDB1 expression levels [adjusted ORs and 95% CIs: 1.92 and 1.11-3.32, 1.48 and 0.85-2.59, 2.00 and 1.15-3.45 for the 2nd-4th quartiles, respectively, compared with the 1st quartile; Ptrend = 0.026]. We also identified a multiplicative interaction between sex and DDB1 expression levels (P = 0.007). Finally, the expanded model with gene expression levels, in addition to demographic and clinical variables, on SCCHN risk was significantly improved, especially among men. In conclusion, reduced DDB1 expression levels were associated with an increased risk of SCCHN. However, these results need to be validated in larger studies.
Paleoecology of Neoproterozoic hypersaline environments: Biomarker evidence for haloarchaea, methanogens, and cyanobacteria

While numerous studies have examined modern hypersaline ecosystems, their equivalents in the geologic past, particularly in the Precambrian, are poorly understood. In this study, biomarkers from ~820 million year (Ma)‐old evaporites from the Gillen Formation of the mid‐Neoproterozoic Bitter Springs Group, central Australia, are investigated to elucidate the antiquity and paleoecology of halophiles. The sediments were composed of alternating laminae of dolomitized microbial mats and up to 90% anhydrite. Solvent extraction of these samples yielded thermally well‐preserved hydrocarbon biomarkers. The regularly branched C25 isoprenoid 2,6,10,14,18‐pentamethylicosane, the tail‐to‐tail linked C30 isoprenoid squalane, and breakdown products of the head‐to‐head linked C40 isoprenoid biphytane, were particularly abundant in the most anhydrite‐rich sediments and mark the oldest current evidence for halophilic archaea. Linear correlations between isoprenoid concentrations (normalized to n‐alkanes) and the anhydrite/dolomite ratio reveal microbial consortia that fluctuated with changing salinity levels. Halophilic archaea were the dominant organisms during periods of high salinity and gypsum precipitation, while bacteria were prevalent during stages of carbonate formation. The irregularly branched C25 isoprenoid 2,6,10,15,19‐pentamethylicosane (PMI), with a central tail‐to‐tail link, was also abundant during periods of elevated salinity, highlighting the activity of methanogens. By contrast, the irregularly branched C20 isoprenoid 2,6,11,15‐tetramethylhexadecane (crocetane) was more common in dolomite‐rich facies, revealing that an alternate group of archaea was active during less saline periods. Elevated concentrations of isotopically depleted heptadecane (n‐C17) revealed the presence of cyanobacteria under all salinity regimes. The combination of biomarkers in the mid‐Neoproterozoic Gillen Formation resembles lipid compositions from modern hypersaline cyanobacterial mats, pointing to a community composition that remained broadly constant since at least the Neoproterozoic. However, as a major contrast to most modern hypersaline environments, the Gillen evaporites did not yield any evidence for algae or other eukaryotes.
Partial volume model for brain MRI scan using MP2RAGE

MP2RAGE is a T1 weighted MRI sequence that estimates a composite image providing much reduction of the receiver bias, has a high intensity dynamic range, and provides an estimate of T1 mapping. It is, therefore, an appealing option for brain morphometry studies. However, previous studies have reported a difference in cortical thickness computed from MP2RAGE compared with widely used Multi‐Echo MPRAGE. In this article, we demonstrated that using standard segmentation and partial volume estimation techniques on MP2RAGE introduces systematic errors, and we proposed a new model to estimate partial volume of the cortical gray matter. We also included in their model a local estimate of tissue intensity to take into account the natural variation of tissue intensity across the brain. A theoretical framework is provided and validated using synthetic and physical phantoms. A repeatability experiment comparing MPRAGE and MP2RAGE confirmed that MP2RAGE using our model could be considered for structural imaging in brain morphology study, with similar cortical thickness estimate than that computed with MPRAGE. Hum Brain Mapp 38:5115–5127, 2017. © 2017 Wiley Periodicals, Inc.
Assessment of mechanical properties of human head tissues for trauma modelling

Many discrepancies are found in the literature regarding the damage and constitutive models for head tissues as well as the values of the constants involved in the constitutive equations. Their proper definition is required for consistent numerical model performance when predicting human head behaviour, and hence skull fracture and brain damage. The objective of this research is to perform a critical review of constitutive models and damage indicators describing human head tissue response under impact loading. A 3D finite element human head model has been generated by using computed tomography images, which has been validated through the comparison to experimental data in the literature. The threshold values of the skull and the scalp that lead to fracture have been analysed. We conclude that (1) compact bone properties are critical in skull fracture, (2) the elastic constants of the cerebrospinal fluid affect the intracranial pressure distribution, and (3) the consideration of brain tissue as a nearly incompressible solid with a high (but not complete) water content offers pressure responses consistent with the experimental data.