bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering kinase–substrate relationships by analysis of domain-specific phosphorylation network
Authors: Damle Nikhil Prakash , Mohanty Debasisa 
Published: February 2014

Motivation: In silico prediction of site-specific kinase–substrate relationships (ssKSRs) is crucial for deciphering phosphorylation networks by linking kinomes to phosphoproteomes. However, currently available predictors for ssKSRs give rise to a large number of false-positive results because they use only a short sequence stretch around phosphosite as determinants of kinase specificity and do not consider the biological context of kinase–substrate recognition.
Results: Based on the analysis of domain-specific kinase–substrate relationships, we have constructed a domain-level phosphorylation network that implicitly incorporates various contextual factors. It reveals preferential phosphorylation of specific domains by certain kinases. These novel correlations have been implemented in PhosNetConstruct, an automated program for predicting target kinases for a substrate protein. PhosNetConstruct distinguishes cognate kinase–substrate pairs from a large number of non-cognate combinations. Benchmarking on independent datasets using various statistical measures demonstrates the superior performance of PhosNetConstruct over ssKSR-based predictors.
Availability and implementation: PhosNetConstruct is freely available at http://www.nii.ac.in/phosnetconstruct.html.
Contact: deb@nii.res.in
Supplementary information: Supplementary Data are available at Bioinformatics online.
Population-based Analysis of Treatment and Survival in Women Presenting With Brain Metastasis at Initial Breast Cancer Diagnosis
Authors: Wiksyk Bradley , Nguyen David H. , Alexander Cheryl , Truong Pauline T. 
Published: February 2014

Purpose:
Brain metastasis at initial breast cancer diagnosis is rare. This study aims to evaluate the clinical characteristics of these patients and identify prognostic and treatment factors associated with improved survival.

Methods:
Subjects were 35 women referred from 1996 to 2005 with newly diagnosed breast cancer with synchronous brain metastasis. Overall survival (OS) and brain progression-free survival were examined using Kaplan-Meier methods and compared between subgroups with different clinicopathologic and treatment characteristics using log-rank tests.

Results:
Median age was 65 years. Whole-brain radiotherapy (WBRT) alone was used in 25 patients, surgical resection and postoperative WBRT in 5 patients, and no or unknown treatment in 5 patients. Patients who underwent cranial resection were more likely to have solitary brain metastasis (P=0.003) and no visceral involvement (P=0.006). Overall, median OS was 6.8 months and median brain progression-free survival was 6.5 months (range, 0.7 to 54 mo). Median OS were 15 months with surgery and postoperative WBRT, 5 months with WBRT alone, and 3 months with no brain treatment. Longer OS was observed with age below 65 years versus 65 years and above (11 vs. 5 mo, P=0.046), 0 to 1 versus ≥2 sites of extracranial metastasis (10 vs. 3 mo, P=0.047), and diagnosis from 2001 to 2005 versus 1996 to 2000 (10 vs. 3 mo, P=0.018). A trend toward improved OS was observed in patients with no visceral involvement (11 vs. 4 mo, P=0.09).

Conclusions:
In this unique cohort presenting with breast cancer and synchronous brain metastasis, longer survival were observed with young age, limited extracranial metastasis, and no visceral disease. These characteristics may be used to select candidates for more aggressive treatment.
A tug-of-war between driver and passenger mutations in cancer and other adaptive processes
Authors: McFarland Christopher , Mirny Leonid , Korolev Kirill S. 
Published: February 2014

AbstractCancer progression is an example of a rapid adaptive process where evolving new traits is essential for survival and requires a high mutation rate. Precancerous cells acquire a few key mutations that drive rapid population growth and carcinogenesis. Cancer genomics demonstrates that these few ‘driver’ mutations occur alongside thousands of random ‘passenger’ mutations—a natural consequence of cancer’s elevated mutation rate. Some passengers can be deleterious to cancer cells, yet have been largely ignored in cancer research. In population genetics, however, the accumulation of mildly deleterious mutations has been shown to cause population meltdown. Here we develop a stochastic population model where beneficial drivers engage in a tug-of-war with frequent mildly deleterious passengers. These passengers present a barrier to cancer progression that is described by a critical population size, below which most lesions fail to progress, and a critical mutation rate, above which cancers meltdown. We find support for the model in cancer age-incidence and cancer genomics data that also allow us to estimate the fitness advantage of drivers and fitness costs of passengers. We identify two regimes of adaptive evolutionary dynamics and use these regimes to rationalize successes and failures of different treatment strategies. We find that a tumor’s load of deleterious passengers can explain previously paradoxical treatment outcomes and suggest that it could potentially serve as a biomarker of response to mutagenic therapies. The collective deleterious effect of passengers is currently an unexploited therapeutic target. We discuss how their effects might be exacerbated by both current and future therapies.
Navigating marine electromagnetic transmitters using dipole field geometry
Authors: Weitemeyer Karen , Constable Steve 
Published: February 2014

ABSTRACTThe marine controlled source electromagnetic (CSEM) technique has been adopted by the hydrocarbon industry to characterize the resistivity of targets identified from seismic data prior to drilling. Over the years, marine controlled source electromagnetic has matured to the point that four‐dimensional or time lapse surveys and monitoring could be applied to hydrocarbon reservoirs in production, or to monitor the sequestration of carbon dioxide. Marine controlled source electromagnetic surveys have also been used to target shallow resistors such as gas hydrates. These novel uses of the technique require very well constrained transmitter and receiver geometry in order to make meaningful and accurate geologic interpretations of the data. Current navigation in marine controlled source electromagnetic surveys utilize a long base line, or a short base line, acoustic navigation system to locate the transmitter and seafloor receivers. If these systems fail, then rudimentary navigation is possible by assuming the transmitter follows in the ship's track. However, these navigational assumptions are insufficient to capture the detailed orientation and position of the transmitter required for both shallow targets and repeat surveys. In circumstances when acoustic navigation systems fail we propose the use of an inversion algorithm that solves for transmitter geometry. This algorithm utilizes the transmitter's electromagnetic dipole radiation pattern as recorded by stationary, close range (<1000 m), receivers in order to model the geometry of the transmitter. We test the code with a synthetic model and validate it with data from a well navigated controlled source electromagnetic survey over the Scarborough gas field in Australia.
Forest fragments modulate the provision of multiple ecosystem services
Authors: Mitchell Matthew G. E. , Bennett Elena M. , Gonzalez Andrew 
Published: February 2014

SummaryAgricultural landscapes provide the essential ecosystem service of food to growing human populations; at the same time, agricultural expansion to increase crop production results in forest fragmentation, degrading many other forest‐dependent ecosystem services. However, surprisingly little is known about the role that forest fragments play in the provision of ecosystem services and how fragmentation affects landscape multifunctionality at scales relevant to land management decisions.We measured the provision of six ecosystem services (crop production, pest regulation, decomposition, carbon storage, soil fertility and water quality regulation) in soya bean fields at different distances from adjacent forest fragments that differed in isolation and size across an agricultural landscape inQuebec,Canada.We observed significant effects of distance‐from‐forest, fragment isolation and fragment size on crop production, insect pest regulation, and decomposition.Distance‐from‐forest and fragment isolation had unique influences on service provision for each of the ecosystem services we measured. For example, pest regulation was maximized adjacent to forest fragments, while crop production was maximized at intermediate distances‐from‐forest. As a consequence, landscape multifunctionality depended on landscape heterogeneity: the range of field and forest fragment types present.We also observed strong negative and positive relationships between ecosystem services that were more prevalent at greater distances‐from‐forest.Synthesis and applications. Our study is one of the first to empirically measure and model the effects of forest fragments on the simultaneous provision of multiple ecosystem services in an agro‐ecosystem at the landscape and field scales relevant to landowners and managers. Our results demonstrate that forest fragments, irrespective of their size, can affect the provision of multiple ecosystem services in surrounding fields, but that this effect is mediated by fragment isolation across the landscape. Our results also suggest that managing habitat fragmentation and landscape structure will improve our ability to optimize ecosystem service provision and create multifunctional agricultural landscapes.
Values beyond value? Is anything beyond the logic of capital?
Authors: Skeggs Bev 
Published: February 2014

AbstractWe are living in a time when it is frequently assumed that the logic of capital has subsumed every single aspect of our lives, intervening in the organization of our intimate relations as well as the control of our time, including investments in the future (e.g. via debt). The theories that document the incursion of this logic (often through the terms of neoliberalism and/or governmentality) assume that this logic is internalized, works and organizes everything including our subjectivity. These theories performatively reproduce the very conditions they describe, shrinking the domain of values and making it subject to capital's logic. All values are reduced to value. Yet values and value are always dialogic, dependent and co‐constituting. In this paper I chart the history by which value eclipses values and how this shrinks our sociological imagination. By outlining the historical processes that institutionalized different organizations of the population through political economy and the social contract, producing ideas of proper personhood premised on propriety, I detail how forms of raced, gendered and classed personhood was formed. The gaps between the proper and improper generate significant contradictions that offer both opportunities to and limits on capitals' lines of flight. It is the lacks, the residues, and the excess that cannot be captured by capital's mechanisms of valuation that will be explored in order to think beyond the logic of capital and show how values will always haunt value.
Association of mannose binding lectin codon 54 polymorphism with predisposition to Henoch–Schönlein purpura in childhood
Authors: Durmaz Burak , Aykut Ayca , Hursitoglu Gultac , Bak Mustafa , Serdaroglu Erkin , Onay Huseyin , Ozkinay Ferda 
Published: February 2014

AbstractAimImmune and inflammatory response activation is a common feature of systemic vasculitis. There is a protein called mannose binding lectin (MBL) that was reported to play an important role in innate immunity. MBL polymorphisms in the MBL gene cause predisposition to infectious and autoimmune diseases. There is no study in the literature investigating the association between MBL polymorphisms and Henoch–Schönlein purpura (HSP) to date. Therefore, the aim of this study is to determine the presence of any association between MBL gene variants and HSP in a child population.MethodCodon 54 polymorphism in exon 1 of the MBL gene was investigated by polymerase chain reaction – restriction fragment length polymorphism method in 100 children diagnosed as having HSP and 100 age‐matched healthy controls.ResultsThe mutant B allele frequency was not significantly higher in the patient group (16%) compared to the control group (14%). AB genotype was found to be 28% and 26% in the patient group and healthy control group, respectively. AA genotype was found in 70% of the children with HSP and 73% of the healthy control group.ConclusionThese results suggest that codon 54 polymorphism in the MBL gene may hardly play a role in susceptibility to HSP in children, the first time this has been reported in the literature.
Does control‐ownership divergence impair market liquidity in an emerging market? Evidence from China
Authors: Chu Xiaojun , Liu Qigui , Tian Gary Gang 
Published: February 2014

AbstractThis paper examines how institutional characteristics of emerging economies influence the effect of control‐ownership divergence on market liquidity. We find that the divergence is negatively associated with liquidity and that this negative relationship is more pronounced in firms with more severe agency problems and information asymmetry. We argue that in an emerging market, the negative effect of the divergence on liquidity is worsened by state ownership and poorer shareholder protection, both of which result in more severe agency conflicts; we also find, however, that this effect is alleviated by the NTS reform, which aligns the interest of different shareholders.
Extensive protein hydrolysate formula effectively reduces regurgitation in infants with positive and negative challenge tests for cow's milk allergy
Authors: Vandenplas Y. , De Greef E. ,   ALLAR study group
Published: February 2014

AbstractAimCow's milk protein allergy (CMPA) is treated using an elimination diet with an extensive protein hydrolysate. We explored whether a thickened or nonthickened version was best for infants with suspected CMPA, which commonly causes regurgitation/vomiting.MethodsDiagnosis of CMPA was based on a positive challenge test. We compared the efficacy of two casein extensive hydrolysates (eCH), a nonthickened version (NT‐eCH) and a thickened version (T‐eCH), using a symptom‐based score covering regurgitation, crying, stool consistency, eczema, urticarial and respiratory symptoms.ResultsA challenge was performed in 52/72 infants with suspected CMPA and was positive in 65.4%. All confirmed CMPA cases tolerated eCH. The symptom‐based score decreased significantly in all infants within a month, and the highest reduction was in those with confirmed CMPA. Regurgitation was reduced in all infants (6.4 ± 3.2–2.8 ± 2.9, p < 0.001), but fell more with the T‐eCH (−4.2 ± 3.2 regurgitations/day vs. −3.0 ± 4.5, ns), especially in infants with a negative challenge (−3.9 ± 4.0 vs. −1.9 ± 3.4, ns).ConclusioneCH fulfilled the criteria for a hypoallergenic formula, and the NT‐eCH and T‐eCH formulas both reduced CMPA symptoms. The symptom‐based score is useful for evaluating how effective dietary treatments are for CMPA.
Robotic retroperitoneal partial nephrectomy: a step‐by‐step guide
Authors: Ghani Khurshid R. , Porter James , Menon Mani , Rogers Craig 
Published: February 2014

ObjectiveTo describe a step‐by‐step guide for successful implementation of the retroperitoneal approach to robotic partial nephrectomy (RPN)Patients and MethodsThe patient is placed in the flank position and the table fully flexed to increase the space between the 12th rib and iliac crest. Access to the retroperitoneal space is obtained using a balloon‐dilating device. Ports include a 12‐mm camera port, two 8‐mm robotic ports and a 12‐mm assistant port placed in the anterior axillary line cephalad to the anterior superior iliac spine, and 7–8 cm caudal to the ipsilateral robotic port.ResultsPositioning and port placement strategies for successful technique include: (i) Docking robot directly over the patient's head parallel to the spine; (ii) incision for camera port ≈1.9 cm (1 fingerbreadth) above the iliac crest, lateral to the triangle of Petit; (iii) Seldinger technique insertion of kidney‐shaped balloon dilator into retroperitoneal space; (iv) Maximising distance between all ports; (v) Ensuring camera arm is placed in the outer part of the ‘sweet spot’.ConclusionThe retroperitoneal approach to RPN permits direct access to the renal hilum, no need for bowel mobilisation and excellent visualisation of posteriorly located tumours.
The association of serum 25‐OH vitamin D with atopy, asthma, and lung function in a prospective study of Danish adults
Authors: Thuesen B. H. , Skaaby T. , Husemoen L. L. N. , Fenger M. , Jørgensen T. , Linneberg A. 
Published: February 2014

SummaryBackgroundBesides the important skeletal functions, it has been suggested that vitamin D is involved in the pathogenesis of allergy and asthma and related to lung function. However, previous studies are inconclusive.ObjectiveThe purpose of this study was to investigate associations of serum levels of 25‐hydroxy vitamin D (25(OH)D) with atopy, asthma, and lung function in a prospective study of Danish adults.MethodsThis study included 4999 adults aged 30–60 years in 1999–2001. Three thousand and thirty‐two of those included at baseline also participated at a follow‐up examination 5 years later, and 3727 answered a 10‐year follow‐up questionnaire. Serum levels of (25(OH)D) were measured by high‐performance liquid chromatography (HPLC) at baseline. No information on use of vitamin D supplements was available. Specific IgE against four common antigens was measured. Information about doctor‐diagnosed asthma was obtained from questionnaires, and lung function (FEV1 and forced vital capacity) was measured by spirometry.ResultsWe found no significant associations of 25(OH)D with atopy and doctor‐diagnosed asthma. However, we found that low levels of 25(OH)D were associated with lower FEV1 percentage predicted (FEV1%pred) in the cross‐sectional analyses. The odds ratio (OR) of FEV1%pred < 80% among participants in the highest quartile of 25(OH)D compared with those in the lowest was 0.66 (95% confidence interval (CI): 0.49–0.74). In contrast, prospective analyses indicated an association between high levels of 25(OH)D at baseline and adverse changes in lung function. OR (95%CI) of incident FEV1%pred < 80% was 1.73 (1.06–2.82) in the highest quartile of 25(OH)D compared with the lowest.Conclusions and Clinical RelevanceOur data indicates that 25(OH)D levels do not influence the development of asthma and allergy among adults. Further, the results did not consistently support that 25(OH)D levels associate with lung function. Randomized controlled trials are needed to further address this issue.
Is routine chestX‐ray after surgical and percutaneous tracheostomy necessary in adults: a systemic review of the current literature
Authors: Yeo W.X. , Phua C.Q. , Lo S. 
Published: February 2014

BackgroundFor many years, routine post‐tracheostomy chestX‐ray has been the standard of care for patients in many countries. However, recent evidence suggests that this is unnecessary and cost‐ineffective.ObjectiveTo review the current literature and examine the role of routine post‐tracheostomy chestX‐ray in adult patients.Type of reviewSystemic review.Search strategyElectronic databases (PubMed,EMBASE, Cochrane) were searched using the keywords ‘chestX‐ray/radiography/radiograph’ and ‘tracheostomy/tracheotomy’ in various permutations. Search period ranged from 1960 to 2012. Inclusion criteria included systematic reviews, meta‐analyses, randomised control trials, prospective and retrospective case series. Paediatric and non‐English articles were excluded. Abstracts and subsequently full text articles were screened by two of the authors independently. References from obtained articles were also examined.Evaluation methodSpecific outcome measures were collated to evaluate the usefulness of post‐tracheostomy chest X‐ray:Chest X‐ray detected (tracheostomy‐related) complication ratesProportion of cases requiring significant interventionPotential predictors of complicationsResultsRoutine post‐tracheostomy chestX‐ray is of a low yield, and its findings had limited impact on patient management. Complication detection rates for surgical and percutaneous tracheostomy are 2.2% and 3.2%, respectively. Only 0.7% and 1.8% of chestX‐rays performed in surgical and percutaneous tracheostomy cases, respectively, required intervention. Certain groups of patients, however, are at higher risks of complications, and may benefit from post‐tracheostomy chestX‐ray. For surgical tracheostomy, these groups include those with post‐operative signs and symptoms of complications or had emergent or ‘difficult’ tracheostomies. For percutaneous tracheostomy, high‐risk patients include trauma cases (unspecified), patients with post‐procedural signs and symptoms of complications, patients who have high ventilatory requirements, difficult tracheostomy cases or tracheostomy cases performed without bronchoscopic guidance.ConclusionThe practice of routine post‐tracheostomy chestX‐ray is debatable owing to its low yield and minimal impact on clinical management. However, certain groups of patients appear to be at higher risks of post‐tracheostomy complications; currently, there is insufficient evidence to conclude the absolute need for routine chestX‐ray in these groups of patients, although it may be prudent to do so based on available evidence in the literature and logical clinical reasoning.
Neural specialization for speech in the first months of life
Authors: Shultz Sarah , Vouloumanos Athena , Bennett Randi H. , Pelphrey Kevin 
Published: February 2014

AbstractHow does the brain's response to speech change over the first months of life? Although behavioral findings indicate that neonates' listening biases are sharpened over the first months of life, with a species‐specific preference for speech emerging by 3 months, the neural substrates underlying this developmental change are unknown. We examined neural responses to speech compared with biological non‐speech sounds in 1‐ to 4‐month‐old infants using fMRI. Infants heard speech and biological non‐speech sounds, including heterospecific vocalizations and human non‐speech. We observed a left‐lateralized response in temporal cortex for speech compared to biological non‐speech sounds, indicating that this region is highly selective for speech by the first month of life. Specifically, this brain region becomes increasingly selective for speech over the next 3 months as neural substrates become less responsive to non‐speech sounds. These results reveal specific changes in neural responses during a developmental period characterized by rapid behavioral changes.