bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Pooled Sequencing Approach Identifies a Candidate Meiotic Driver inDrosophila
Authors: Wei Kevin H-C , Reddy Hemakumar M , Rathnam Chandramouli , Lee Jimin , Lin Deanna , Ji Shuqing , Mason James M , Clark Andrew G , Barbash Daniel A 
Published: March 2017

AbstractMendel’s Law of equal segregation states that each of the two alleles in a diploid organism has an equal probability of being transmitted into...Meiotic drive occurs when a selfish element increases its transmission frequency above the Mendelian ratio by hijacking the asymmetric divisions of female meiosis. Meiotic drive causes genomic conflict and potentially has a major impact on genome evolution, but only a few drive loci of large effect have been described. New methods to reliably detect meiotic drive are therefore needed, particularly for discovering moderate-strength drivers that are likely to be more prevalent in natural populations than strong drivers. Here, we report an efficient method that uses sequencing of large pools of backcross (BC1) progeny to test for deviations from Mendelian segregation genome-wide with single-nucleotide polymorphisms (SNPs) that distinguish the parental strains. We show that meiotic drive can be detected by a characteristic pattern of decay in distortion of SNP frequencies, caused by recombination unlinking the driver from distal loci. We further show that control crosses allow allele-frequency distortion caused by meiotic drive to be distinguished from distortion resulting from developmental effects. We used this approach to test whether chromosomes with extreme telomere-length differences segregate at Mendelian ratios, as telomeric regions are a potential hotspot for meiotic drive due to their roles in meiotic segregation and multiple observations of high rates of telomere sequence evolution. Using four different pairings of long and short telomere strains, we find no evidence that extreme telomere-length variation causes meiotic drive in Drosophila. However, we identify one candidate meiotic driver in a centromere-linked region that shows an ∼8% increase in transmission frequency, corresponding to a ∼54:46 segregation ratio. Our results show that candidate meiotic drivers of moderate strength can be readily detected and localized in pools of BC1 progeny.
Germ Granules Prevent Accumulation of Somatic Transcripts in the AdultCaenorhabditis elegansGermline
Authors: Knutson Andrew Kekūpa’a , Egelhofer Thea , Rechtsteiner Andreas , Strome Susan 
Published: March 2017

AbstractGerm granules are widely conserved, germ-cell-specific, ribonucleo protein organelles. In C. elegans, germ granules (P granules) are necessary for fertility...The germ cells of multicellular organisms protect their developmental potential through specialized mechanisms. A shared feature of germ cells from worms to humans is the presence of nonmembrane-bound, ribonucleoprotein organelles called germ granules. Depletion of germ granules in Caenorhabditis elegans (i.e., P granules) leads to sterility and, in some germlines, expression of the neuronal transgene unc-119::gfp and the muscle myosin MYO-3. Thus, P granules are hypothesized to maintain germ cell totipotency by preventing somatic development, although the mechanism by which P granules carry out this function is unknown. In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P granule-depleted gonads at different developmental stages. Our results demonstrate that P granules are necessary for adult germ cells to downregulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs. P granule-depleted gonads that express the unc-119::gfp transgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers. Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to cause germ cells to express UNC-119::GFP and MYO-3 and to display RNA accumulation defects similar to those observed after depletion of P granules. Our data identify P granules as critical modulators of the germline transcriptome and guardians of germ cell fate.
The Bacterial Sequential Markov Coalescent
Authors: De Maio Nicola , Wilson Daniel J 
Published: March 2017

Abstract
Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e., using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)—an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is available from https://bitbucket.org/nicofmay/fastsimbac, and is distributed as open source under the terms of the GNU General Public License. Lastly, we use the BSMC within an Approximate Bayesian Computation (ABC) inference scheme, and suggest that parameters simulated under the exact CGC can correctly be recovered, further showcasing the accuracy of the BSMC. With this ABC we infer recombination rate, mutation rate, and recombination tract length of Bacillus cereus from a whole genome alignment.
Annealing of Complementary DNA Sequences During Double-Strand Break Repair inDrosophilaIs Mediated by the Ortholog of SMARCAL1
Authors: Holsclaw Julie Korda , Sekelsky Jeff 
Published: March 2017

AbstractDNA double-strand breaks (DSBs) pose a serious threat to genomic integrity. If unrepaired, they can lead to chromosome fragmentation and cell death. If repaired incorrectly, they can cause mutations and chromosome rearrangements. DSBs are repaired using end-joining or homology-directed repair strategies, with the predominant form of homology-directed repair being synthesis-dependent strand annealing (SDSA). SDSA is the first defense against genomic rearrangements and information loss during DSB repair, making it a vital component of cell health and an attractive target for chemotherapeutic development. SDSA has also been proposed to be the primary mechanism for integration of large insertions during genome editing with CRISPR/Cas9. Despite the central role for SDSA in genome stability, little is known about the defining step: annealing. We hypothesized that annealing during SDSA is performed by the annealing helicase SMARCAL1, which can anneal RPA-coated single DNA strands during replication-associated DNA damage repair. We used unique genetic tools in Drosophila melanogaster to test whether the fly ortholog of SMARCAL1, Marcal1, mediates annealing during SDSA. Repair that requires annealing is significantly reduced in Marcal1 null mutants in both synthesis-dependent and synthesis-independent (single-strand annealing) assays. Elimination of the ATP-binding activity of Marcal1 also reduced annealing-dependent repair, suggesting that the annealing activity requires translocation along DNA. Unlike the null mutant, however, the ATP-binding defect mutant showed reduced end joining, shedding light on the interaction between SDSA and end-joining pathways.
Perth, unreal city
Authors: Stratton Jon 
Published: March 2017

There are a surprising number of songs that reference Perth, Western Australia, written by artists who do not live there and who might have visited, usually on tour, or have never been there at all. In this article I examine the reasons for this, suggesting that Perth is a city that has become very mythic. This mythic investment is a consequence of Perth being in the west of Australia—California has some of the same mythic qualities in the United States—being (almost) on the coast, and on the coast of the ocean not a sea, and being constructed as isolated. This article examines the impact of these mythic tropes through a reading of various song lyrics where Perth is either in the title or in the lyrics, or both. These include songs by Gordon Lightfoot, Beirut, Bon Iver and Pavement among others.
A study on diabetic foot and its association with peripheral artery disease
Authors: Muthiah Alli , Kandasamy Ramachandran , S. Nagulan , Madasamy Aruna 
Published: March 2017

Background: Diabetes mellitus is characterized by high blood sugar levels over a prolonged period due to alteration in either the insulin secretion, insulin action, or both. Worldwide, as of the recent 2016 data collected from the World Health Organization (WHO) around 422 million adults have diabetes mellitus which is estimated to almost double by 2030 which is composed of mainly type 2 diabetes (85-90% of all cases). The early detection of peripheral artery disease in asymptomatic patients goes a long way in reduction of major lower limb amputations and mortality. Hence, there is a need for evaluation of peripheral vascular disease in all diabetics, especially those with diabetic foot by formulating effective management protocols, thereby limiting the morbidity, mortality and social costs associated with the disease.Methods: Patients admitted and seen in out-patient department for diabetic foot ulcers between January 2013 and October 2013 in Department of general surgery, vascular surgery and diabetology, Kilpauk Medical College Hospital, Chennai, India were taken for study.Results: 150 cases satisfying the inclusion criteria were taken up for the study from January 2013 to October 2013. Out of 150 patients, 76 patients presented with ulcer in foot, 34 presented with gangrene of toe or foot. After clinical examination it was found that 52 patients had associated neuropathy, 17 patients had ABI less than 0.3 and 39 patients had ABI in between 0.4 and 0.9. Patients with ulcer and gangrene in foot and with ABI less than 0.9 were admitted and evaluated with doppler study of lower limbs. After getting consent, appropriate procedure was done for each patient. Wound debridement was done in 21 cases, toe disarticulation in 12, fore foot amputations in 4, Below knee amputation in 9, above knee amputation in 3. 11 patients were referred to vascular surgery and underwent revascularization procedures (BYPASS).Conclusions: The prevalence of peripheral artery disease in patients with diabetic foot is significantly high i.e. 38 % as per this study. Males have a higher predilection for developing peripheral vascular disease than females. The average age of presentation of PAD in diabetics is 40 -60 years. The most common level of arterial occlusion in PAD associated diabetic foot is femoro-popliteal segment followed by tibial segment.
Outcome of harmonic scalpel circumcision in children with hemophilia
Authors: Mohamed Wael Barakaat Ahmed , Ali Mustafa Ahmed , Abou-Taleb Ashraf 
Published: March 2017

Background: There are many techniques described to decrease the risk of bleeding after circumcision in patients with bleeding diathesis such as monopolar diathermy, bipolar scissors and fibrin glue. Up to our knowledge, no previous study described the use of the harmonic scalpel in patients with bleeding diathesis. Our aim was to evaluate postoperative outcome after harmonic scalpel circumcision in boys with hemophilia.Methods: This was a prospective observational study carried out in Sohag University Hospitals, Sohag, Egypt. The patients were recruited from Outpatient pediatric hematology clinic from January 2014 till January 2017. All procedures were done under general anesthesia. After strict sterilization, the dorsal aspect of the prepuce was incised using harmonic scalpel up to the coronal sulcus, then the whole prepuce was cut circumferentially using the harmonic scalpel. It is a sutureless technique.Results: 26 boys with hemophilia A and 5 with hemophilia B were included. Their median age was 5 and 8 years respectively. The most common indication for circumcision was religious (20/31), the intraoperative blood loss ranged between 0-5 ml, operative time ranged between 3-5 minutes, there was no intraoperative complication, one case of rebleeding managed conservatively by factor administration, two cases of wound infection responded to antibiotic therapy, hospital stay ranged between 1-3 days. It was a sutureless technique.Conclusions: Harmonic scalpel circumcision is a safe technique in children with hemophilia, it decreased the risk of rebleeding, decreased operative time and it is also a sutureless technique and may decrease the cost by reducing the amount of factor replacement.
Plot-scale assessment of soil freeze/thaw detection and variability with impedance probes: implications for remote sensing validation networks
Authors: Williamson Matthew , Adams Justin R. , Berg Aaron A. , Derksen Chris , Toose Peter , Walker Anne 
Published: March 2017

AbstractSeveral large in-situ soil moisture-monitoring networks currently exist over seasonally frozen regions that may have use for the validation of remote sensing soil freeze/thaw (F/T) products. However, further understanding of how the existing network instrumentation responds to changes in near surface soil F/T is recommended. This case study describes the results of a small plot-scale (7 × 7 m) study from November 2013 through April 2014 instrumented with 36 impedance probes. Soil temperature and real dielectric permittivity ϵr' were measured every 15 minutes during F/T transition periods at shallow soil depths (0–10 cm). Categorical soil temperature and real dielectric permittivity techniques were used to define the soil F/T state during these periods. Results demonstrate that both methods for detecting soil F/T have strong agreement (84.7–95.6%) during the fall freeze but weak agreement (53.3–60.9%) during the spring thaw. Bootstrapping results demonstrated both techniques showed a mean difference within ±1.0°C and ±1.4 ϵr' between the standard 5 cm below surface measurement depth and probes at 2, 10 and integrated 0–5.7 cm depths installed within the same study plot. Overall this study demonstrates that the Hydra Probe offers promise for near surface soil F/T detection using existing soil moisture monitoring networks particularly for the fall freeze.
Groundwater quality modeling using neuro-particle swarm optimization and neuro-differential evolution techniques
Authors: Kisi Ozgur , Keshavarzi Ali , Shiri Jalal , Zounemat-Kermani Mohammad , Omran El-Sayed Ewis 
Published: March 2017

Abstract
Recently, the capabilities of artificial neural networks (ANNs) in simulating dynamic systems have been proven. However, the common training algorithms of ANNs (e.g., back-propagation and gradient algorithms) are featured with specific drawbacks in terms of slow convergence and probable entrapment in local minima. Alternatively, novel training techniques, e.g., particle swarm optimization (PSO) and differential evolution (DE) algorithms might be employed for conquering these shortcomings. In this paper, ANN-PSO and ANN-DE models were applied for modeling groundwater qualitative parameters, i.e., SO4 and sodium adsorption ratio (SAR). Three statistical parameters including root mean square error (RMSE), mean absolute error (MAE), and the coefficient of determination (R2) were used for assessing the models' capabilities. The results showed that the ANN-DE presents more accurate results than ANN-PSO in modeling SAR and electrical conductivity (EC).
Regional aspects of streamflow droughts in the Andean rivers of Patagonia, Argentina. Links with large-scale climatic oscillations
Authors: Rivera Juan Antonio , Araneo Diego C. , Penalba Olga C. , Villalba Ricardo 
Published: March 2017

AbstractUnder the current global warming trend, droughts are expected to increase, with serious implications for water resources management. This study analyzed the regional aspects of droughts in terms of streamflow deficiencies over the Andean rivers of Patagonia, Argentina. Based on the variable threshold level method, the main characteristics of streamflow droughts were obtained for the hydrological years 1962/63–2014/15, considering three different severity levels over 11 representative basins. Two distinct regional behaviors were identified in terms of temporal variations of streamflow drought duration and its cumulative deficit volume, dividing the study area into North and Central Patagonia. The effects of the Southern Annular Mode (SAM), the El Niño–Southern Oscillation (ENSO), and the Pacific Decadal Oscillation (PDO) on the interannual and interdecadal variability of streamflow droughts were assessed through an empirical decomposition applied to the regional time series. These large-scale climatic oscillations have a distinct regional and temporal behavior in terms of the modulation of streamflow drought variability. Considering the interannual streamflow drought variability, the El Niño signal is more consistent and contributes with humid conditions, especially over North Patagonia. The multi-decadal component of the streamflow drought time series is linked to the upward trend in SAM, particularly over Central Patagonia.
Extreme event characterization for the river basins of Eastern Indian Gangetic Plains
Authors: Yaduvanshi Aradhana , Sinha Anand Kr 
Published: March 2017

Abstract
The Eastern Indian Gangetic Plains are characterized by a primarily nature-dependent region blessed with an enormous supply of mineral resources. The region is witnessing a rapid transition in its demographic structure because of rapid industrialization. The region provides a classic example of an area which shows a trend reverse to that observed globally, as far as the frequency of extreme precipitation events is concerned. This paper provides a risk characterization of the entire region, based on the empirical behavior shown by data available so far, in addition to predictions based on theory of extreme values. The long-term behavior prediction is made with an aim to provide policy makers ample time and direction to develop suitable disaster prevention measures. The focus is primarily on extremely high rainfall events, their frequency, trend and estimated long-term behavior. The study corroborates the stability assumption behind the Indian monsoon, and also provides an indication of the expected long-term as well as short-term threats. This study provides a unique application of the extreme value theory to help in developing a threat map for a region whose population is known to be highly impacted by any significant deviations from a normal monsoon.
Determining discharge coefficient of labyrinth and arced labyrinth weirs using support vector machine
Authors: Roushangar Kiyoumars , Alami Mohammad Taghi , Shiri Jalal , Asl Mahdi Majedi 
Published: March 2017

Abstract
A labyrinth weir is a linear weir folded in plan-view which increases the crest length and the flow rate for a given channel width and an upstream flow depth. The present study aimed at determining discharge coefficients of labyrinth and arced labyrinth weirs using support vector machine (SVM)-based models. A total of 527 laboratory test data of four types of weirs, namely, Normal and Inverted orientation Labyrinth Weirs in flume (NLW, ILW) and Arced Labyrinth Weirs with and without nappe Breakers in reservoir (ALW, ALWB), were captured from the published literature and utilized to feed the SVM-based models. The obtained results revealed the capability of the SVM-based models in determining discharge coefficients. The results showed that the SVM-based model of arced labyrinth weir (ALW) produced the most accurate results when three dimensionless parameters, e.g. (HT/P) head water ratio, (α/θ) angle ratio and (Lc/W) magnification ratio, were introduced as input parameters (Root mean square error [RMSE]= 0.013 and R2 = 0.970 for the test stage). Nonetheless, sensitivity analysis showed that Froude number and head water ratio are the most influential parameters on discharge coefficients of the labyrinth and arced labyrinth weirs, respectively.
Soil moisture and temperature dynamics in typical alpine ecosystems: a continuous multi-depth measurements-based analysis from the Qinghai-Tibet Plateau, China
Authors: Zhang Si-Yi , Li Xiao-Yan 
Published: March 2017

Abstract
Soil temperature and moisture are the key variables that control the overall effect of climate and topography on soil and vegetation in alpine regions. However, there has been little investigation of the potential soil temperature and moisture feedbacks on climate changes in different alpine ecosystems and their impact on vegetation change. Soil temperature and moisture at five depths were measured continuously at 10-min intervals in three typical ecosystems (Kobresia meadow (KMd), Achnatherum splendens steppe (ASSt), and Potentilla fruticosa shrub (PFSh)) of the Qinghai Lake watershed on the northeast Qinghai-Tibet Plateau, China. The findings of this study revealed that the KMd and PFSh sites had relatively low soil temperature and high soil moisture, whereas the ASSt site had relatively warm soil temperature and low soil moisture. The soil and vegetation characteristics had important effects on the infiltration process and soil moisture regime; about 47%, 87%, and 34% of the rainfall (minus interception) permeated to the soil in the KMd, PFSh, and ASSt sites, respectively. In the context of the warming climate, changes to soil moisture and temperature are likely to be the key reasons of the alpine meadow deterioration and the alpine shrub expansion in the alpine regions.