bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence comparison of the mitochondrial genomes of Plesionika species (Caridea: Pandalidae), gene rearrangement and phylogenetic relationships of Caridea
Authors: Sun Yuman , Chen Jian , Liang Xinjie , Li Jiji , Ye Yingying , Xu Kaida 
Published: May 2024

Background
Despite the Caridean shrimps’ vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes.

Methods
The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina’s next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank.

Results
The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species—P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group.

Conclusions
Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.
Abiotic processes control carbon dioxide dynamics in temperate karst lakes
Authors: Vargas-Sánchez Mariana , Alcocer Javier , Puche Eric , Sánchez-Carrillo Salvador 
Published: May 2024

Inland waters are crucial in the carbon cycle, contributing significantly to the global CO2 fluxes. Carbonate lakes may act as both sources and sinks of CO2 depending on the interactions between the amount of dissolved inorganic carbon (DIC) inputs, lake metabolisms, and geochemical processes. It is often difficult to distinguish the dominant mechanisms driving CO2 dynamics and their effects on CO2 emissions. This study was undertaken in three groundwater-fed carbonate-rich lakes in central Spain (Ruidera Lakes), severely polluted with nitrates from agricultural overfertilization. Diel and seasonal (summer and winter) changes in CO2 concentration (CCO2) DIC, and CO2 emissions-(FCO2)-, as well as physical and chemical variables, including primary production and phytoplanktonic chlorophyll-a were measured. In addition, δ13C-DIC, δ13C-CO2 in lake waters, and δ13C of the sedimentary organic matter were measured seasonally to identify the primary CO2 sources and processes. While the lakes were consistently CCO2 supersaturated and FCO2 was released to the atmosphere during both seasons, the highest CCO2 and DIC were in summer (0.36–2.26 µmol L–1). Our results support a strong phosphorus limitation for primary production in these lakes, which impinges on CO2 dynamics. External DIC inputs to the lake waters primarily drive the CCO2 and, therefore, the FCO2. The δ13C-DIC signatures below –12‰ confirmed the primary geogenic influence on DIC. As also suggested by the high values on the calcite saturation index, the Miller-Tans plot revealed that the CO2 source in the lakes was close to the signature provided by the fractionation of δ13C-CO2 from calcite precipitation. Therefore, the main contribution behind the CCO2 values found in these karst lakes should be attributed to the calcite precipitation process, which is temperature-dependent according to the seasonal change observed in δ13C-DIC values. Finally, co-precipitation of phosphate with calcite could partly explain the observed low phytoplankton production in these lakes and the impact on the contribution to increasing greenhouse gas emissions. However, as eutrophication increases and the soluble reactive phosphorus (SRP) content increases, the co-precipitation of phosphate is expected to be progressively inhibited. These thresholds must be assessed to understand how the CO32− ions drive lake co-precipitation dynamics. Carbonate regions extend over 15% of the Earth’s surface but seem essential in the CO2 dynamics at a global scale.
Temperature-size responses during ontogeny are independent of progenitors’ thermal environments
Authors: Martínez-De León Gerard , Fahrni Micha , Thakur Madhav P. 
Published: May 2024

Background
Warming generally induces faster developmental and growth rates, resulting in smaller asymptotic sizes of adults in warmer environments (a pattern known as the temperature-size rule). However, whether temperature-size responses are affected across generations, especially when thermal environments differ from one generation to the next, is unclear. Here, we tested temperature-size responses at different ontogenetic stages and in two consecutive generations using two soil-living Collembola species from the family Isotomidae: Folsomia candida (asexual) and Proisotoma minuta (sexually reproducing).

Methods
We used individuals (progenitors; F0) from cultures maintained during several generations at 15 °C or 20 °C, and exposed their offspring in cohorts (F1) to various thermal environments (15 °C, 20 °C, 25 °C and 30 °C) during their ontogenetic development (from egg laying to first reproduction; i.e., maturity). We measured development and size traits in the cohorts (egg diameter and body length at maturity), as well as the egg diameters of their progeny (F2). We predicted that temperature-size responses would be predominantly determined by within-generation plasticity, given the quick responsiveness of growth and developmental rates to changing thermal environments. However, we also expected that mismatches in thermal environments across generations would constrain temperature-size responses in offspring, possibly due to transgenerational plasticity.

Results
We found that temperature-size responses were generally weak in the two Collembola species, both for within- and transgenerational plasticity. However, egg and juvenile development were especially responsive at higher temperatures and were slightly affected by transgenerational plasticity. Interestingly, plastic responses among traits varied non-consistently in both Collembola species, with some traits showing plastic responses in one species but not in the other and vice versa. Therefore, our results do not support the view that the mode of reproduction can be used to explain the degree of phenotypic plasticity at the species level, at least between the two Collembola species used in our study. Our findings provide evidence for a general reset of temperature-size responses at the start of each generation and highlight the importance of measuring multiple traits across ontogenetic stages to fully understand species’ thermal responses.
Cash Transfers and Social Vulnerability in Bosnia: A Cross-sectional Study of Households and Listed Beneficiaries
Authors: Andersson Neil , Paredes-Solis Sergio , Sherr Lorraine , Cockcroft Anne 
Published: January 2011

AbstractObjectivePromoted as a means of fueling markets and encouraging economic growth or recovery, cash transfers have become a popular approach to international assistance. The literature recognizes potential problems such as insecurity, corruption, misuse, gender inequality, market inflation, and ineffective targeting. We carried out population and beneficiary surveys in 1997 to evaluate the targeting of cash transfers in Bosnia soon after the end of the conflict.MethodsThe population survey visited a random sample of clusters from population registers in Bosnia and Herzegovina (BiH) and Republika Srpska (RS). A directly administered questionnaire asked households whether they received any cash handouts from the Municipal Welfare Office in the last year, and, if so, for what purpose, the amount, and how they used the money. We calculated coverage and inclusion and exclusion errors of the program. The field team also identified cash transfers beneficiaries from official lists of the program and attempted to contact a random sample of them to ask about their experience.ResultsIt was not possible to confirm receipts of cash in one third of the sample of 840 named beneficiaries; 19% could not be traced and 17% of those found denied receiving any cash. In the general population survey of 7182 households, coverage rates with cash assistance (11% in BiH, 3% in RS) were at least 44% lower than those declared by the distribution agencies, with considerable variation between cantons. Exclusion errors were high: 83% of those eligible according to the program's income criterion did not receive any cash. Although sufficient cash was dispensed to reach every United Nations High Commission for Refugees priority 1 (most needy) household, only 13% of these households (278/2125) admitted receiving any cash. Inclusion errors were also high: 60% of all of those who received cash were not in the priority 1 category and 46% were not eligible according to the program's income criterion. Extrapolating from the population survey findings, we could only account for a maximum of US$4 million received by households in BiH and RS up to May 1997, of the US$16 million dispersed by the program up to that time.ConclusionsTargeting of the cash transfers program was poor, with large inclusion and exclusion errors. Much of the disbursed cash apparently did not reach the intended beneficiaries and could not be accounted for. Agencies on the ground did not have the necessary skills to handle the disbursements or to train national organizations to do so. (Disaster Med Public Health Prepardness. 2013;7:232-240)
Analysis of Mitochondrial DNA Point Mutation Heteroplasmy by ARMS Quantitative PCR
Authors: Wang Jing , Venegas Victor , Li Fangyuan , Wong Lee‐Jun 
Published: January 2011

AbstractMitochondrial disorders are a group of complex and heterogeneous diseases that may be caused by molecular defects in both the nuclear and mitochondrial genomes. Pathogenic mitochondrial DNA (mtDNA) mutations are usually present in the heteroplasmic form. The degree of mtDNA mutation heteroplasmy (mutation load) varies among different tissues. Manifestation of clinical phenotypes depends on the mutation load in affected tissues. Thus, it is important to quantify the degree of mutation heteroplasmy in various tissues. This unit outlines the design of allele refractory mutation system (ARMS)‐based quantitative PCR (qPCR) analysis of three common mtDNA point mutations. This is a cost‐effective and sensitive single‐step method to simultaneously detect and quantify heteroplasmic mtDNA point mutations. It requires as little as 0.1 ng of total genomic DNA per reaction and can be used to quantify mutation heteroplasmy in various noninvasively obtained tissues such as hair follicles, buccal swab, and urine sediment. Detailed protocols for ARMS primer design and qPCR set up, validation procedures, and cautions in the interpretation of results, as well as advantages and limitations are discussed. ARMS qPCR is an important tool for addressing some of the diagnostic challenges of mitochondrial disease. Curr. Protoc. Hum. Genet. 68:19.6.1‐19.6.16 © 2011 by John Wiley & Sons, Inc.
Mutations in the TSGA14 gene in families with autism spectrum disorders
Authors: Korvatska O. , Estes A. , Munson J. , Dawson G. , Bekris L.M. , Kohen R. , Yu C.‐E. , Schellenberg G.D. , Raskind W.H. 
Published: January 2011

AbstractLinkage to 7q has been the most robust genetic finding in familial autism. A previous scan of multiplex families with autism spectrum disorders found a linkage signal of genome‐wide significance at D7S530 on 7q32. We searched a candidate imprinted region at this location for genetic variants in families with positive linkage scores. Using exon resequencing, we identified three rare potentially pathogenic variants in the TSGA14 gene, which encodes a centrosomal protein. Two variants were missense mutations (c.664C>G; p.P206A and c.766T>G; p.C240G) that changed conserved residues in the same protein domain; the third variant (c.192+5G>A) altered splicing, which resulted in a protein with an internal deletion of 16 residues and a G33D substitution. These rare TSGA14 variants are enriched in the affected subjects (6/348 patients versus 2/670 controls, Fisher's exact two tailed P = 0.022). This is the first report of a possible link of a gene with a centrosomal function with familial autism. © 2011 Wiley‐Liss, Inc.
Body mass and stature estimation based on the first metatarsal in humans
Authors: De Groote Isabelle , Humphrey Louise T. 
Published: January 2011

AbstractArchaeological assemblages often lack the complete long bones needed to estimate stature and body mass. The most accurate estimates of body mass and stature are produced using femoral head diameter and femur length. Foot bones including the first metatarsal preserve relatively well in a range of archaeological contexts. In this article we present regression equations using the first metatarsal to estimate femoral head diameter, femoral length, and body mass in a diverse human sample. The skeletal sample comprised 87 individuals (Andamanese, Australasians, Africans, Native Americans, and British). Results show that all first metatarsal measurements correlate moderately to highly (r= 0.62–0.91) with femoral head diameter and length. The proximal articular dorsoplantar diameter is the best single measurement to predict both femoral dimensions. Percent standard errors of the estimate are below 5%. Equations using two metatarsal measurements show a small increase in accuracy. Direct estimations of body mass (calculated from measured femoral head diameter using previously published equations) have an error of just over 7%. No direct stature estimation equations were derived due to the varied linear body proportions represented in the sample. The equations were tested on a sample of 35 individuals from Christ Church Spitalfields. Percentage differences in estimated and measured femoral head diameter and length were less than 1%. This study demonstrates that it is feasible to use the first metatarsal in the estimation of body mass and stature. The equations presented here are particularly useful for assemblages where the long bones are either missing or fragmented, and enable estimation of these fundamental population parameters in poorly preserved assemblages. Am J Phys Anthropol, 2011. © 2011 Wiley‐Liss, Inc.
Fracture toughness of polyamide 6/maleated ethylene–propylene–diene terpolymer rubber/nano calcium carbonate ternary composites according to essential work of fracture analysis
Authors: Fu Li‐Dan , Chen Si , Wang Yong‐Jie , Wang Xiao‐Dong , Wang Xu 
Published: January 2011

AbstractPolyamide 6 (PA6)/maleated ethylene–propylene–diene terpolymer rubber/nano calcium carbonate ternary composites were prepared. The effect of the compounding route on the morphology, toughness, and fracture behavior of the ternary composites were investigated by scanning electron microscopy, Charpy impact testing, and essential work of fracture (EWF) testing. The construction of sandbag microstructure particles in PA6 matrix was crucial to the toughness of the ternary composites. The Charpy impact strength and the specific essential work of fracture (we) of the ternary composites with a sandbag microstructure were 137.9 and 71.4% higher, respectively, than those of the ordinary ternary composites with a separated dispersion microstructure. The observation of the fracture surface after EWF testing indicated that the improvement of we was attributed to the sandbag microstructure particles; this structure was more effective for resisting the growth of cracks; meanwhile, the influence of the amount of fibrillation on the nonspecific essential work of fracture, including the nonspecific essential work of fracture before yielding and that in the necking–tearing stage, was insignificant. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Synthesis, modification, and porous properties of new glycidyl methacrylate copolymers
Authors: Podkościelna Beata 
Published: January 2011

AbstractSynthesis, copolymerization, and physicochemical properties of new, of different degrees of crosslinker tetrafunctional bis[4(2‐hydroxy‐3‐methacryloyloxypropoxy)phenyl]sulfide and glycidyl methacrylate copolymers are presented. The monomers were used for the synthesis of porous microspheres in the presence of pore‐forming diluents, decan‐1‐ol, and toluene. Influence of diluents composition on their porous structures was studied. Porous structure of the obtained microspheres in dry (from nitrogen adsorption–desorption measurements) states was studied. Their chemical structures were studied by the use of Fourier transform infrared. The number of epoxy groups of the obtained copolymers, their thermal properties (thermogravimetric analysis), and swelling characteristics in 10 solvents of different chemical nature were examined. Selected copolymers were modified by amines in the epoxide ring‐opening reaction. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Sulfur containing poly(N‐isopropylacrylamide) copolymer hydrogels for thermosensitive extraction of gold(III) ions
Authors: Hemvasdukij Suwimol , Ngeontae Wittaya , Imyim Apichat 
Published: January 2011

AbstractPoly[N‐isopropylacrylamide‐co‐[2‐(methylthio)ethyl methacrylate]], poly(NIPA‐co‐MTEMA) gels were prepared by free radical polymerization in aqueous solution. The homogeneous and heterogeneous gels were prepared by using 10 mM MTEMA in 5.0%(v/v) ethanol at 10°C and 30 mM MTEMA in 20%(v/v) ethanol at 50°C, in 1.0 and 1.5M NIPA solution, respectively. Homogeneous and heterogeneous gels had swelling ratios at 540 ± 28% and 551 ± 37%, respectively. The extraction of Au(III) ion was studied in batch method. The optimum pHs for the extraction of Au(III) by homogeneous and heterogeneous gels were 1–3 and 1–5, respectively. The suitable extraction time was 3 h at 50°C when using a rod‐shaped copolymer (0.7 cm diameter and 1 cm length). The adsorption behavior obeyed the Langmuir and Freundlich isotherms. The maximum sorption capacities of Au(III) onto homogeneous and heterogeneous gels were 62.8 and 322 μmol/g, respectively. The desorption equilibrium was reached within 2–3 h at 10°C by 0.1M thiourea in 5%(v/v) HCl. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Volumetric Reconstruction of the Mouse Meibomian Gland Using High‐Resolution Nonlinear Optical Imaging
Authors: Jester Bryan E. , Nien Chyong JY , Winkler Moritz , Brown Donald J. , Jester James V. 
Published: January 2011

AbstractNon‐linear optical array tomography generated volume rendering of the mouse meibomian gland (green) with a single orthogonal section through the 3‐D reconstruction (Red‐Blue Heat map). Tissue section shows interstitial collagen detected by second harmonic generation that was used to generate a meibomian gland mask to segment out the meibomian gland cells detected by two photon excited fluorescence. See Jester et al., on page 185, in this issue.
Stereological Assessment of Developing Mouse Ovarian Follicles in an in vitro Culture System
Authors: Chand Ashwini , Legge Michael 
Published: January 2011

AbstractThe aim of this project was to validate the use of ovarian follicular diameter measurement as an indicator of growth using stereology as an independent measure. A strong linear correlation was observed between follicular volume and diameter, and between follicular volume and the total number of granulosa cells. These results have provided a useful validation of a widely used technique for determining follicular growth in vitro. Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.
The saturation of galactic dynamos
Authors: Moss D. , Sokoloff D. 
Published: January 2011

AbstractWe summarize the current state of the long term discussion about the saturation mechanisms associated with rapid growth of small‐scale magnetic field, that operate in large‐scale galactic dynamos, and related problems with magnetic helicity conservation. Our general conclusion is that, taking into account magnetic helicity fluxes, large‐scale magnetic field can be amplified up to about the equipartition level. In contrast, models without helicity fluxes give an initial temporal magnetic field growth, but then decay. In our opinion, it is more appropriate to refer to the situation as a “potentially catastrophic scenario” rather than as “catastrophic α‐quenching” (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Energy oscillations and a possible route to chaos in a modified Riga dynamo
Authors: Stefani F. , Gailitis A. , Gerbeth G. 
Published: January 2011

AbstractStarting from the present version of the Riga dynamo experiment with its rotating magnetic eigenfield dominated by a single frequency we ask for those modifications of this set‐up that would allow for a non‐trivial magnetic field behaviour in the saturation regime. Assuming an increased ratio of azimuthal to axial flow velocity, we obtain energy oscillations with a frequency below the eigenfrequency of the magnetic field. These new oscillations are identified as magneto‐inertial waves that result from a slight imbalance of Lorentz and inertial forces. Increasing the azimuthal velocity further, or increasing the total magnetic Reynolds number, we find transitions to a chaotic behaviour of the dynamo (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Differential rotation and meridional flow of Arcturus
Authors: Küker M. , Rüdiger G. 
Published: January 2011

AbstractThe spectroscopic variability of Arcturus hints at cyclic activity cycle and differential rotation. This could provide a test of current theoretical models of solar and stellar dynamos. To examine the applicability of current models of the flux transport dynamo to Arcturus, we compute a mean‐field model for its internal rotation, meridional flow, and convective heat transport in the convective envelope. We then compare the conditions for dynamo action with those on the Sun. We find solar‐type surface rotation with about 1/10th of the shear found on the solar surface. The rotation rate increases monotonically with depth at all latitudes throughout the whole convection zone. In the lower part of the convection zone the horizontal shear vanishes and there is a strong radial gradient. The surface meridional flow has maximum speed of 170 m/s and is directed towards the equator at high and towards the poles at low latitudes. Turbulent magnetic diffusivity is of the order 1015–1016 cm2/s. The conditions on Arcturus are not favorable for a circulation‐dominated dynamo (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)