bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species
Authors: Zhang Yeting , Fernandez-Aparicio Monica , Wafula Eric K , Das Malay , Jiao Yuannian , Wickett Norman J , Honaas Loren A , Ralph Paula E , Wojciechowski Martin F , Timko Michael P , Yoder John I , Westwood James H , dePamphilis Claude W 
Published: February 2013

Abstract

Background
Parasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown.

Results
Here we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique “disulfide through disulfide knot” structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants.

Conclusions
The HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.
Change of urinary fluoride and bone metabolism indicators in the endemic fluorosis areas of southern china after supplying low fluoride public water
Authors: Chen Shaoxian , Li Boling , Lin Shao , Huang Yixiang , Zhao Xinhua , Zhang Min , Xia Yuan , Fang Xiaoheng , Wang Junyi , Hwang Syni-An , Yu Shouyi 
Published: February 2013

Abstract

Background
Few studies have evaluated health impacts, especially biomarker changes, following implementation of a new environmental policy. This study examined changes in water fluoride, urinary fluoride (UF), and bone metabolism indicators in children after supplying low fluoride public water in endemic fluorosis areas of Southern China. We also assessed the relationship between UF and serum osteocalcin (BGP), calcitonin (CT), alkaline phosphatase (ALP), and bone mineral density to identify the most sensitive bone metabolism indicators related to fluoride exposure.

Methods
Four fluorosis-endemic villages (intervention villages) in Guangdong, China were randomly selected to receive low-fluoride water. One non-endemic fluorosis village with similar socio-economic status, living conditions, and health care access, was selected as the control group. 120 children aged 6-12 years old were randomly chosen from local schools in each village for the study. Water and urinary fluoride content as well as serum BGP, CT, ALP and bone mineral density were measured by the standard methods and compared between the children residing in the intervention villages and the control village. Benchmark dose (BMD) and benchmark dose lower limit (BMDL) were calculated for each bone damage indicator.

Results
Our study found that after water source change, fluoride concentrations in drinking water in all intervention villages (A-D) were significantly reduced to 0.11 mg/l, similar to that in the control village (E). Except for Village A where water change has only been taken place for 6 years, urinary fluoride concentrations in children of the intervention villages were lower or comparable to those in the control village after 10 years of supplying new public water. The values of almost all bone indicators in children living in Villages B-D and ALP in Village A were either lower or similar to those in the control village after the intervention. CT and BGP are sensitive bone metabolism indicators related to UF. While assessing the temporal trend of different abnormal bone indicators after the intervention, bone mineral density showed the most stable and the lowest abnormal rates over time.

Conclusions
Our results suggest that supplying low fluoride public water in Southern China is successful as measured by the reduction of fluoride in water and urine, and changes in various bone indicators to normal levels. A comparison of four bone indicators showed CT and BGP to be the most sensitive indicators.
Development of neurodevelopmental disorders: a regulatory mechanism involving bromodomain-containing proteins
Authors: Li Junlin , Zhao Guifang , Gao Xiaocai 
Published: February 2013

AbstractNeurodevelopmental disorders are classified as diseases that cause abnormal functions of the brain or central nervous system. Children with neurodevelopmental disorders show impaired language and speech abilities, learning and memory damage, and poor motor skills. However, we still know very little about the molecular etiology of these disorders. Recent evidence implicates the bromodomain-containing proteins (BCPs) in the initiation and development of neurodevelopmental disorders. BCPs have a particular domain, the bromodomain (Brd), which was originally identified as specifically binding acetyl-lysine residues at the N-terminus of histone proteinsin vitroandin vivo. Other domains of BCPs are responsible for binding partner proteins to form regulatory complexes. Once these complexes are assembled, BCPs alter chromosomal states and regulate gene expression. Some BCP complexes bind nucleosomes, are involved in basal transcription regulation, and influence the transcription of many genes. However, most BCPs are involved in targeting. For example, some BCPs function as a recruitment platform or scaffold through their Brds-binding targeting sites. Others are recruited to form a complex to bind the targeting sites of their partners. The regulation mediated by these proteins is especially critical during normal and abnormal development. Mutant BCPs or dysfunctional BCP-containing complexes are implicated in the initiation and development of neurodevelopmental disorders. However, the pathogenic molecular mechanisms are not fully understood. In this review, we focus on the roles of regulatory BCPs associated with neurodevelopmental disorders, including mental retardation, Fragile X syndrome (FRX), Williams syndrome (WS), Rett syndrome and Rubinstein-Taybi syndrome (RTS). A better understanding of the molecular pathogenesis, based upon the roles of BCPs, will lead to screening of targets for the treatment of neurodevelopmental disorders.
Extensive bowel resection in infancy is another cause of increasing plasma alphafetoprotein concentration
Authors: Wojtulewicz Julian , Coakley John 
Published: February 2013

Background Plasma alphafetoprotein (AFP) concentrations are high at birth and decline progressively to reach adult levels between eight and 24 months of age. AFP is an important tumour marker for hepatoblastoma but may also increase following hepatic resection. The liver and intestine have similar embryonic origins from endoderm, so we postulated that plasma AFP may also rise after extensive bowel resection. Methods AFP was measured postoperatively in plasma in four infants who had undergone resections of large amounts of intestine. AFP was measured twice in two babies and multiple times in the other two. Results In three of the four infants, the AFP concentrations were markedly above the expected levels for age, and in all four babies, AFP concentrations rose when they may have been expected to fall. Conclusion Rising plasma AFP concentrations post extensive bowel resection in infants is a new finding which is possibly due to intestinal regeneration.
Alternative Calibration Strategies for the Clinical Laboratory: Application to Nortriptyline Therapeutic Drug Monitoring
Authors: Olson Matthew T , Breaud Autumn , Harlan Robert , Emezienna Nkechinyere , Schools Sabitha , Yergey Alfred L , Clarke William 
Published: February 2013

BACKGROUND
The addition of a calibration curve with every run is both time-consuming and expensive for clinical mass spectrometry assays. We present alternative calibration strategies that eliminate the need for a calibration curve except as required by laboratory regulations.

METHODS
We measured serum nortriptyline concentrations prospectively in 68 patients on 16 days over a 2-month period using a method employing calibration schemes that relied on the measurement of the response ratio (RR) corrected by the response factor (RF), i.e., a measurement of the RR for an equimolar mixture of the analyte and internal standard. Measurements were taken with contemporaneous RF (cRF) measurements as well as sporadic RF (sRF) measurements. The measurements with these alternative calibration schemes were compared against the clinical results obtained by interpolation on a calibration curve, and those differences were evaluated for analytical and clinical significance.

RESULTS
The differences between the values measured by cRF and sRF calibration and interpolation on a calibration curve were not significant (P = 0.088 and P = 0.091, respectively). Both the cRF- and sRF-based calibration results demonstrated a low mean bias against the calibration curve interpolations of 3.69% (95% CI, −15.8% to 23.2%) and 3.11% (95% CI, −16.4% to 22.6%), respectively. When these results were classified as subtherapeutic, therapeutic, or supratherapeutic, there was categorical agreement in 95.6% of the cRF calibration results and 94.1% of the sRF results.

CONCLUSIONS
cRF and sRF calibration in a clinically validated liquid chromatography–tandem mass spectrometry assay yields results that are analytically and clinically commensurate to those produced by interpolation with a calibration curve.
Nielsen numbers of maps of aspherical figure-eight type polyhedra
Authors: Yi Peter , Kim Seung Won 
Published: February 2013

Abstract
Let X be an aspherical polyhedron of the homotopy type
of the figure-eight and let f : X → X be a self-map. The Wagner
algorithm [Trans. Amer. Math. Soc. 351 (1999), 41–62] provides computations for the Nielsen number of
self-maps of X satisfying the remnant condition. If f is without
remnant, then using the concept of mutant by Jiang [Math. Ann. 311 (1998), 467–479] we may assume
that f
#(b) is an initial segment of f
#(a), where f
# is
the induced endomorphism of π1(X) and a, b are generators of
π1(X). Let f
#(b) = U and f
#(a) = Un

R, where n is the
maximal such positive integer. If R is not an initial segment of
U, we say that f is of Type Y. In this paper, we prove that if
f is of Type Y, then f can be mutated either to a map that has
remnant or to an exceptional form for which we can calculate the
Nielsen number directly. Not all self-maps of X are of Type Y. However, making use of the results in this paper, an algorithm is
presented by Kim [J. Pure Appl. Algebra 216 (2012),
1652–1666] that does compute the Nielsen number for
all self-maps of X.
Anxious and depressive components of Edinburgh Postnatal Depression Scale in maternal postpartum psychological problems1)
Authors: Petrozzi Angela , Gagliardi Luigi 
Published: February 2013

Abstract

Background: The Edinburgh Postnatal Depression Scale (EPDS) is a widely used instrument for screening for postpartum depression, but it might also detect anxiety symptoms.

Objective: To investigate the factor structure of the EPDS administered immediately after delivery and to understand which factors predict a high EPDS score 3 months later.

Methods: A cohort of 594 Italian mothers delivering a healthy baby at Versilia Hospital completed the EPDS at two points in time: 2 days after delivery (T0) and 3 months later (T1) by telephone interview.

Results: EPDS scores were higher at T0 than at T1. Overall, 15.7% of women at 2 days postpartum and 7.6% at 3 months later reported a score >9. The factor analysis of EPDS at T0 indicated a three-factor structure: “depression” (items 7–10), “anxiety” (items 3–6) and “anhedonia” (items 1–2). Anxious symptoms were quantitatively more important than depressive ones (mean 3.9 vs. 1.2) but tended to spontaneously ameliorate at T1, whereas total EPDS score at T1 was better predicted by depressive symptoms at T0 (discriminative ability 0.75 vs. 0.68).

Conclusions: This study suggests that EPDS subscales immediately after delivery help understand the spectrum of maternal postpartum psychological problems. Anxious symptoms immediately after delivery are frequent but transient, linked probably to maternity blues or atypical depression, whereas the presence of depressive symptomatology at T0 suggests higher risk of later depressive disorders.
Self-consistent Scale-bridging Approach to Compute the Elasticity of Multi-phase Polycrystalline Materials
Authors: Titrian Hajjir , Aydin Ugur , Friák Martin , Ma Duancheng , Raabe Dierk , Neugebauer Jörg 
Published: February 2013

ABSTRACTA necessary prerequisite for a successful theory-guided up-scale design of materials with application-driven elastic properties is the availability of reliable homogenization techniques. We report on a new software tool that enables us to probe and analyze scale-bridging structure-property relations in the elasticity of materials. The newly developed application, referred to as SC-EMA (Self-consistent Calculations of Elasticity of Multi-phase Aggregates) computes integral elastic response of randomly textured polycrystals. The application employs a Python modular library that uses single-crystalline elastic constants Cij as input parameters and calculates macroscopic elastic moduli (bulk, shear, and Young's) and Poisson ratio of both single-phase and multi-phase aggregates. Crystallites forming the aggregate can be of cubic, tetragonal, hexagonal, orthorhombic, or trigonal symmetry. For cubic polycrystals the method matches the Hershey homogenization scheme. In case of multi-phase polycrystalline composites, the shear moduli are computed as a function of volumetric fractions of phases present in aggregates. Elastic moduli calculated using the analytical self-consistent method are computed together with their bounds as determined by Reuss, Voigt and Hashin-Shtrikman homogenization schemes. The library can be used as (i) a toolkit for a forward prediction of macroscopic elastic properties based on known single-crystalline elastic characteristics, (ii) a sensitivity analysis of macro-scale output parameters as function of input parameters, and, in principle, also for (iii) an inverse materials-design search for unknown phases and/or their volumetric ratios.
Effect of Audio Clips of Heavily Accented Lecture on Teacher Evaluations
Authors: Choo Freddie , Tan Kim B. 
Published: February 2013

ABSTRACT:
This study examines the relation between using audio clips of a nonnative, English-speaking instructor's heavily accented lecture (hereafter, HAL) and student evaluations of the instructor's teaching. In Spring 2011, we recorded audio clips of our HAL and made them available to students through iLearn, a learning management system. We found a significant positive relation between audio clips usage and several improved teacher evaluation ratings. This finding is useful to nonnative, English-speaking instructors because accounting students are influential in teacher evaluations, and the majority of accounting administrators in the United States use teacher evaluations for decisions on retention, promotion, and tenure.
Data Availability: Available upon request.
Evaluation of somatic and functional parameters of cardiovascular and respiratory systems in rural women in Poland
Authors: Ignasiak Tomasz , Ignasiak Zofia , Ziółkowska-Łajp Ewa , Rożek Krystyna , Sławińska Teresa , Skrzek Anna 
Published: February 2013

The aim of this study was the diagnosis of selected somatic parameters and functional parameters of cardiovascular and respiratory systems of rural women in Poland. The study involved a group of 95 rural women aged 35–60 years, staying in 3-week rehabilitation camps. The two groups of women were selected: younger (x=43 years), which did not exceed 50 years of age (n=48) and older (x=53 years) aged 50 years and older (n=47). The present study examines the measurement of the body height and weight, Body Mass Index (BMI) and functional parameters of cardiovascular and respiratory systems. For the evaluation of cardiovascular parameters, a 6 minute walk test was selected. Before the commencement of the test and in the first minute after it, the pulse and the blood pressure were measured. To assess the functional parameters of the respiratory system, the pattern of flow – volume curve was used. The test was performed with a Jaeger Flowscreen spirometer. The following parameters were determined: forced vital capacity (FVC), forced expiratory volume in one second (FEV1), peak expiratory flow (PEF) and Tiffeneau index (FEV1 in% VC).
Examined rural women were likely to be similar to their urban counterparts. BMI of women was significantly higher than peers. Older rural women are particularly at risk of obesity. Heart rate and blood pressure, when at resting and after exercise, were normal and alike in both in young and older women. As expected, younger women had significantly higher levels of respiratory parameters. PEF values in younger women were slightly below the normal limit, and in their older peers, this value was significantly below the normal limit.
On three rugose coral genera from Serpukhovian strata in the Upper Silesian Coal Basin, Poland
Authors: Fedorowski Jerzy 
Published: February 2013

ABSTRACT
Fedorowski, J. 2012. On three rugose coral genera from Serpukhovian strata in the Upper Silesian Coal Basin, Poland. Acta Geologica Polonica, 62 (1), 1-33. Warszawa
The rugose coral specimens included by Schindewolf (1952) in the genera Claviphyllum Hudson, 1942, Fasciculophyllum Thomson, 1883 and Pentaphyllum (Tachylasma) Grabau, 1922 are revised on the basis of the original collection. The first two taxa are included in Antiphyllum Schindewolf, 1952, either in its original sense or in its newly introduced subgenus Antiphyllites. The new genus Effigies is introduced for Pentaphyllum (Tachylasma ) silesiacum Schindewolf, 1952. The reasons for placing individual genera within given families and suborders are discussed. New, detailed descriptions of species are supplemented by text-figures in order to document their intraspecific variability and phylogenetic relationships.
Geochemical and stable isotope patterns of calcite cementation in the Upper Cretaceous Chalk, Uk: Direct evidence from calcite-filled vugs in brachiopods
Authors: Hu Xiufang , Jeans Christopher , Dickson Tony 
Published: February 2013

ABSTRACT
Hu, X-F, Jeans, C.V. and Dickson, J.A.D. 2012. Geochemical and stable isotope patterns of calcite cementation in the Upper Cretaceous Chalk, UK: Direct evidence from calcite-filled vugs in brachiopods. Acta GeologicaPolonica, 62 (2), 143-172. Warszawa. The history of research into the cementation of the Upper Cretaceous Chalk of the UK is reviewed. Calcitefilled vugs within the shell cavities of terebratulid brachiopods from the Cenomanian Chalk of eastern England have been investigated by cathodoluminesence imaging, staining, electron microprobe and stable isotope analysis. This has provided the first detailed analysis of the geochemistry of the Chalk’s cement. Two cement series, suboxic and anoxic, are recognized. Both start with a Mg-rich calcite with positive δ 13 C values considered to have been precipitated under oxic conditions influenced by aerobic ammonification. The suboxic series is characterized by positive δ 13 C values that became increasingly so as cementation progressed, reaching values of 3.5‰. Manganese is the dominant trace element in the earlier cement, iron in the later cement. Mnand Fe-reducing microbes influenced cement precipitation and the trace element and δ 13 C patterns. The anoxic series is characterized by δ 13 C values that became increasingly negative as cementation progressed, reaching values of -6.5‰. Trace elements are dominated by iron and manganese. Sulphate-reducing microbes influenced cement precipitation and the trace element and δ 13 C patterns. Both cement series are related closely to lithofacies and early lithification pre-dating the regional hardening of the Chalk. The suboxic series occurs in chalk which was continuously deposited and contained hematite pigment and limited organic matter. The anoxic series was associated with slow to nil deposition and hardground development in chalks that originally contained hematite pigment but no longer do so, and an enhanced supply of organic matter.
Faunal dynamics of foraminiferal assemblages in the Bathonian (Middle Jurassic) ore-bearing clays at Gnaszyn, Kraków-Silesia Homocline, Poland
Authors: Smoleń Jolanta 
Published: February 2013

ABSTRACT
Smoleń, J. 2012. Faunal dynamics of foraminiferal assemblages in the Bathonian (Middle Jurassic) ore-bearing clays at Gnaszyn, Kraków-Silesia Homocline, Poland. Acta Geologica Polonica, 62(3), 403-419. Warszawa.
The faunal dynamics of benthic foraminifera in the Middle Jurassic ore-bearing clays of Gnaszyn (Kraków- Częstochowa Upland, south-central Poland) are used to reconstruct sedimentary environments. Two types of foraminiferal assemblages, distinct in their quantitative and qualitative composition, were distinguished; type I assemblages, characterizing intervals between horizons with sideritic concretions; and type II assemblages, characterising horizons with sideritic concretions. Benthic foraminifers were further subdivided into eight ecological morphogroups, based on their morphological features and micro-habitats. Type I assemblages consist mostly of plano/concavo-convex, small-sized epifaunal morphotypes, with a restricted occurrence of shallow infaunal forms and a scarcity of deep infaunal taxa, which suggests low-oxygen conditions in both sediment and bottom waters, and a high sedimentation rate in an outer shelf environment. Type II assemblages are characterized by high taxonomic diversity, high specimen abundance and variability of epifaunal and infaunal morphotypes representing a mixed group of specialized feeding strategies. This suggests optimum living conditions controlled by a lower sedimentation rate, relatively well-oxygenated bottom waters and sufficient or high food supply.