bluuebunny/crossref_metadata_2025_split huggingface dataset:
A two-qubit photonic quantum processor and its application to solving systems of linear equations
Authors: Barz Stefanie , Kassal Ivan , Ringbauer Martin , Lipp Yannick Ole , Dakić Borivoje , Aspuru-Guzik Alán , Walther Philip 
Published: August 2014

AbstractLarge-scale quantum computers will require the ability to apply long sequences of entangling gates to many qubits. In a photonic architecture, where single-qubit gates can be performed easily and precisely, the application of consecutive two-qubit entangling gates has been a significant obstacle. Here, we demonstrate a two-qubit photonic quantum processor that implements two consecutive CNOT gates on the same pair of polarisation-encoded qubits. To demonstrate the flexibility of our system, we implement various instances of the quantum algorithm for solving of systems of linear equations.
TRPC1 contributes to the Ca2+-dependent regulation of adenylate cyclases
Authors: Willoughby Debbie , Ong Hwei Ling , De Souza Lorena Brito , Wachten Sebastian , Ambudkar Indu S. , Cooper Dermot M. F. 
Published: August 2014

SOCE (store-operated Ca2+ entry) is mediated via specific plasma membrane channels in response to ER (endoplasmic reticulum) Ca2+ store depletion. This route of Ca2+ entry is central to the dynamic interplay between Ca2+ and cAMP signalling in regulating the activity of Ca2+-sensitive adenylate cyclase isoforms (AC1, AC5, AC6 and AC8). Two proteins have been identified as key components of SOCE: STIM1 (stromal interaction molecule 1), which senses ER Ca2+ store content and translocates to the plasma membrane upon store depletion, where it then activates Orai1, the pore-forming component of the CRAC (Ca2+ release-activated Ca2+) channel. Previous studies reported that co-expression of STIM1 and Orai1 in HEK-293 (human embryonic kidney 293) cells enhances Ca2+-stimulated AC8 activity and that AC8 and Orai1 directly interact to enhance this regulation. Nonetheless, the additional involvement of TRPC (transient receptor potential canonical) channels in SOCE has also been proposed. In the present study, we evaluate the contribution of TRPC1 to SOCE-mediated regulation of Ca2+-sensitive ACs in HEK-293 cells stably expressing AC8 (HEK-AC8) and HSG (human submandibular gland) cells expressing an endogenous Ca2+-inhibited AC6. We demonstrate a role for TRPC1 as an integral component of SOCE, alongside STIM1 and Orai1, in regulating Ca2+ fluxes within AC microdomains and influencing cAMP production.
Effect of woody-plant encroachment on livestock production in North and South America
Authors: Anadón José D. , Sala Osvaldo E. , Turner B. L. , Bennett Elena M. 
Published: August 2014

Significance
Grasslands all over the world are undergoing a rapid shift from herbaceous to woody-plant dominance, a phenomenon known as woody-plant encroachment. The impact of this global phenomenon on livestock production (LP), the main ecosystem service provided by grasslands, remains largely unexplored. We quantified, for the first time, the impact of woody-plant encroachment on LP at a large scale, finding a reduction of between 0.6 and 1.6 reproductive cows per square kilometer for each 1% increase in tree cover. By comparing the largest rangelands of the Americas (United States and Argentina), we also showed how the impact of woody-plant encroachment is mediated by social–economic factors. Our paper represents a significant advance in our understanding of grasslands as complex social–ecological systems.
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers
Authors: Perry George H. , Foll Matthieu , Grenier Jean-Christophe , Patin Etienne , Nédélec Yohann , Pacis Alain , Barakatt Maxime , Gravel Simon , Zhou Xiang , Nsobya Sam L. , Excoffier Laurent , Quintana-Murci Lluis , Dominy Nathaniel J. , Barreiro Luis B. 
Published: August 2014

Significance
Tropical rainforest hunter-gatherer populations worldwide share the pygmy phenotype, or small human body size. The evolutionary history of this phenotype is largely unknown. Here we studied DNA from the Batwa, a rainforest hunter-gatherer population from east central Africa, to identify regions of the Batwa genome that underlie the pygmy phenotype. We then performed population genomic analyses to study the evolution of these regions, including comparisons with the Baka, a west central African rainforest hunter-gatherer population. We conclude that the pygmy phenotype likely arose due to positive natural selection and that it arose possibly multiple times within Africa. These results support longstanding anthropological hypotheses that small body size confers an important selective advantage for human rainforest hunter-gatherers.
UV damage-induced RNA polymerase II stalling stimulates H2B deubiquitylation
Authors: Mao Peng , Meas Rithy , Dorgan Kathleen M. , Smerdon Michael J. 
Published: August 2014

Significance
It is unknown how (or if) the chromatin landscape responds to transcription stalling to signal rescue of arrested RNA polymerase II (RNAPII). This study identifies a chromatin response to DNA damage-induced RNAPII arrest, the rapid deubiquitylation of histone H2B. This response is an important step for fine-tuning the chromatin landscape to allow the occurrence of DNA repair while avoiding excess RNAPII degradation. Our finding sheds light on the rescue of stalled RNAPII in the context of chromatin, illuminating the involvement of H2B deubiquitylation in coordinating different rescue pathways. Importantly, defects in RNAPII rescue are a phenotype of the human disease Cockayne syndrome, which is characterized by photosensitivity, neurological degeneration, and premature aging.
Trachyandesitic volcanism in the early Solar System
Authors: Bischoff Addi , Horstmann Marian , Barrat Jean-Alix , Chaussidon Marc , Pack Andreas , Herwartz Daniel , Ward Dustin , Vollmer Christian , Decker Stephan 
Published: August 2014

Significance
Volcanism is a fundamental geological process on planets and was substantial during crustal growth on planetary bodies in the early Solar System, as witnessed by ubiquitous rocks of basaltic composition, e.g., on Earth, Moon, Mars, and asteroids. Besides basaltic volcanism, trachyandesite lavas are generated on Earth. The first occurrence of a trachyandesite lava in the meteorite collections demonstrates that trachyandesitic, alkali-, and silica-rich volcanism takes place not only on Earth today but already occurred on a small planetesimal ∼4.56 billion years ago. It sets new constraints on mechanisms and styles of early Solar System volcanism.
Gyrification from constrained cortical expansion
Authors: Tallinen Tuomas , Chung Jun Young , Biggins John S. , Mahadevan L. 
Published: August 2014

Significance
The convolutions of the human brain are a symbol of its functional complexity and correlated with its information-processing capacity. Conversely, loss of folds is correlated with loss of function. But how did the outer surface of the brain, the layered cortex of neuronal gray matter, get its folds? Guided by prior experimental observations of the growth of the cortex relative to the underlying white matter, we argue that these folds arise due to a mechanical instability of a soft tissue that grows nonuniformly. Numerical simulations and physical mimics of the constrained growth of the cortex show how compressive mechanical forces sculpt it to form characteristic sulci and gyri, consistent with observations across species in both normal and pathological situations.
Adaptive growth factor delivery from a polyelectrolyte coating promotes synergistic bone tissue repair and reconstruction
Authors: Shah Nisarg J. , Hyder Md. Nasim , Quadir Mohiuddin A. , Dorval Courchesne Noémie-Manuelle , Seeherman Howard J. , Nevins Myron , Spector Myron , Hammond Paula T. 
Published: August 2014

Significance
A critical challenge in the field of tissue repair is effective bone repair and reconstruction. The clinical standard of extracting bone from another area in the body or from donors is severely hampered by short supply, pain, and concerns about disease transmission. In this study, we developed a polymer-based nanolayered coating that carries active biological drugs in physiologically relevant amounts for tissue repair, with tunable release properties to induce bone repair. Using a rodent model, we observed that these coatings yield mature, mechanically stable bone that bridges large defects and restores the native form. This system is a potent strategy for safe and precise tissue repair and has the potential to significantly boost successful outcomes for bone repair.
A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer
Authors: Gallon Matthew , Clairfeuille Thomas , Steinberg Florian , Mas Caroline , Ghai Rajesh , Sessions Richard B. , Teasdale Rohan D. , Collins Brett M. , Cullen Peter J. 
Published: August 2014

Significance
Cell surface proteins are regulated by a constant cycle of internalization and recycling from intracellular compartments called endosomes. From these organelles, two protein sorting platforms, sorting nexin 27 (SNX27) and the retromer complex, play a critical role in the retrieval of various proteins responsible for ion transport, glucose metabolism, neurotransmission, and other cell functions. Based on the three-dimensional structure of SNX27 in complex with the retromer subunit VPS26, we define the mechanism by which these proteins cooperate to drive endosomal cargo sorting. Retromer and SNX27 dysfunction is implicated in various disorders, including diabetes, Down syndrome, Parkinson disease, and Alzheimer’s disease, and this work provides important insights into the assembly of this essential endosomal sorting machinery.
Narcolepsy patients have antibodies that stain distinct cell populations in rat brain and influence sleep patterns
Authors: Bergman Peter , Adori Csaba , Vas Szilvia , Kai-Larsen Ylva , Sarkanen Tomi , Cederlund Andreas , Agerberth Birgitta , Julkunen Ilkka , Horvath Beata , Kostyalik Diana , Kalmár Lajos , Bagdy Gyorgy , Huutoniemi Anne , Partinen Markku , Hökfelt Tomas 
Published: August 2014

Significance
Narcolepsy is a chronic sleep disease with autoimmune origin. We explored occurrence of autoantibodies in narcolepsy and other sleep-related disorders (OSRDs) by screening human sera with immunohistochemistry on rat brains. Hypocretin/orexinergic neurons were not stained, but a prominent immunostaining pattern of hypothalamic melanin-concentrating hormone (MCH) and proopiomelanocortin (POMC) neurons was overrepresented in cases of narcolepsy and OSRD patients. The autoantigen was identified as the common C-terminal epitope of neuropeptide glutamic acid-isoleucine/α–melanocyte-stimulating hormone (NEI/αMSH). Purified IgGs from a patient with MCH/POMC staining injected intracerebroventricularly to rats caused disturbed sleep patterns. Also, GABAergic cortical interneurons were stained with other narcolepsy and OSRD sera. Thus, autoantibodies are frequent in patients with sleep disorders, and NEI/αMSH may be a previously unidentified autoantigen involved in pathomechanism(s). These findings indicate possible diagnostic/therapeutic targets.
Electrostatics-driven shape transitions in soft shells
Authors: Jadhao Vikram , Thomas Creighton K. , Olvera de la Cruz Monica 
Published: August 2014

SignificanceShape is a fundamental property of an object that influences its interaction with the environment and often determines the object’s functional capabilities. Understanding how to generate and control shape by modifying the environmental conditions is of primary importance in designing systems that respond to external cues. We show here that electrostatic interactions can be used to change the equilibrium shape of soft, nanometer-sized shells. We find that a uniformly charged, spherical shell undergoes shape changes, transforming into ellipsoids, discs, and bowls, as the electrolyte concentration in the environment is decreased. This electrostatics-based shape design mechanism, regulated by varying properties external to the shell, can be used to build efficient nanocontainers for various medical and technological applications.
CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data
Authors: Ramazzotti Daniele , Caravagna Giulio , Loohuis Loes Olde , Graudenzi Alex , Korsunsky Ilya , Mauri Giancarlo , Antoniotti Marco , Mishra Bud 
Published: August 2014

AbstractWe devise a novel inference algorithm to effectively solve thecancer progression model reconstructionproblem. Our empirical analysis of the accuracy and convergence rate of our algorithm,CAncer PRogression Inference(CAPRI), shows that it outperforms the state-of-the-art algorithms addressing similar problems.MotivationSeveral cancer-related genomic data have become available (e.g.,The Cancer Genome Atlas, TCGA) typically involving hundreds of patients. At present, most of these data are aggregated in across-sectionalfashion providing all measurements at the time of diagnosis.Our goal is to infer cancer “progression” models from such data. These models are represented as directed acyclic graphs (DAGs) of collections of “selectivity” relations, where a mutation in a geneA“selects” for a later mutation in a geneB. Gaining insight into the structure of such progressions has the potential to improve both the stratification of patients and personalized therapy choices.ResultsThe CAPRI algorithm relies on a scoring method based on aprobabilistic theorydeveloped by Suppes, coupled withbootstrapandmaximum likelihoodinference. The resulting algorithm is efficient, achieves high accuracy, and has good complexity, also, in terms of convergence properties. CAPRI performs especially well in the presence of noise in the data, and with limited sample sizes. Moreover CAPRI, in contrast to other approaches, robustly reconstructs different types of confluent trajectories despite irregularities in the data.We also report on an ongoing investigation using CAPRI to studyatypical Chronic Myeloid Leukemia, in which we uncovered non trivial selectivity relations and exclusivity patterns among key genomic events.AvailabilityCAPRI is part of theTRanslational ONCOlogyR package and is freely available on the web at:http://bimib.disco.unimib.it/index.php/TroncoContactdaniele.ramazzotti@disco.unimib.it
Dual autogenous control of the multiple antibiotic resistance phenotype inEscherichia coli
Authors: Rodrigo Guillermo , Bajić Djordje , Elola Ignacio , Poyatos Juan F. 
Published: August 2014

AbstractBacteria can defend against diverse antibiotics by mounting a multiple antibiotic resistance (mar) phenotype. The resistance is linked to a chromosomal locus that encodes an activator and a repressor regulating their own expression. Here, we investigated how this dual autogenous control determines the dynamics of the response. We found that the regulatory architecture provides a mechanism to enable rapid induction, generate pulses of activation, and increase the range of sensing. The response is also graded and homogeneous across the population. Moreover, the interaction of a third regulator with the core module fine tunes the previous features, while limiting the cross-talk with metabolic signals. A minimal model accurately anticipates these properties, and emphasizes how specific attributes of the circuit components constrain the appearance of other potential behaviors associated to the regulatory design. Our results integrate both molecular and circuit-level characteristics to fully elucidate the dynamic emergence of themarphenotype.
Ac-Cent-Tchu-Ate the positive
Authors: M. Watson Ann 
Published: August 2014

Purpose
– The purpose of this column is to address how utilizing positive psychology can be beneficial in solving complex problems and increasing staff productivity.

Design/methodology/approach
– This is a viewpoint column.

Findings
– Many academic libraries, along with their parent institutions, are facing difficult challenges. Finding ways to maintain a positive outlook can be beneficial in meeting these obstacles and keeping staff motivated and productive.

Originality/value
– This column addresses how the author’s history of reading self-help books has been beneficial in providing leadership tools and in helping overcome challenging circumstances in academic libraries.
Reward systems promote high-performance work teams achieving library mission
Authors: D. Hall-Ellis Sylvia 
Published: August 2014

Purpose
– The purpose of this paper is to discuss that development and recognition of human capital is a shared responsibility reflecting a delicate balance with employees on one side and the organization on the other. Conveying the message that employees matter, are valued contributors and will be rewarded improves morale, builds trust and expands opportunities for growth, through challenging assignments, improving performance and furthering skill development.

Design/methodology/approach
– The typical organizational structure in a library is made up of three key components: formal reporting relationships, the identification of groupings of individuals into departments or teams and the design of systems that ensures effective communication, coordination and integration of efforts across units. What steps can a library administrator take to reimagine and implement a responsive rewards system?

Findings
– There are five recommendations for library administrators to develop and implement a rewards system.

Originality/value
– New thought piece on this topic.
Can a mentoring program save you money?
Authors: A. Crumpton Michael 
Published: August 2014

Purpose
– The purpose of this article is to suggest that a benefit-cost analysis should be performed for mentoring activities so as to justify the effort and expense and as a tool for measuring effectiveness.

Design/methodology/approach
– Pulling from field literature, this article provides some examples of mentoring programs and resources as well as an example for conducting an analysis.

Findings
– The author feels that applying a cost model to mentoring programs can strengthen their appeal overall.

Originality/value
– The article and its conclusions are the product of this author and his experiences with such programs.
Work characteristics and work performance of knowledge workers
Authors: Hernaus Tomislav , Mikulić Josip 
Published: August 2014

Purpose– The purpose of this paper is to investigate a specific pattern of relationships among various task, knowledge and social characteristics of work design and work outcomes. It clearly shows how particular work characteristics influence task and contextual performance.Design/methodology/approach– The empirical research was conducted through a field survey of the largest Croatian organizations with more than 500 employees. A cross-sectional and cross-occupational sample of 512 knowledge workers from 48 organizations is analyzed by applying the partial least squares structural equation modeling technique.Findings– The results confirmed the existence and importance of the interaction between work characteristics and work outcomes. However, the findings suggest that only knowledge characteristics of work design exhibit a significant effect on both dimensions of work behavior, while task and social characteristics showed different effects on task and contextual performance, respectively.Practical implications– The research findings clearly show that work design efforts are not straightforward but rather context-specific, and with diverging performance effects. Organizations can significantly enhance their bottom-line performance by designing challenging and cognitively demanding configurations of work tasks for their knowledge workers.Originality/value– The paper extends previous research by capturing a broader set of work characteristics of knowledge workers. The results suggest that different categories of work characteristics have different effects on task and contextual performance. By revealing the nature of work design in the central and eastern European context, this study indicates the existence of possible differences in work design practices in various backgrounds.
Paradigm debates and marketing theory, thought and practice
Authors: Tadajewski Mark 
Published: August 2014

Purpose– This paper aims to provide a history of a number of intellectual debates in marketing theory and consumer research. It outlines the key arguments involved, highlights the politics and acrimoniousness that often accompanied the competition for academic prestige or practitioner remuneration. It weaves the contents of the special issue into its narrative.Design/methodology/approach– This article engages in a broad historical survey of the history of marketing thought, as it pertains to intellectual debate and disputation.Findings– While scholars often articulate objectivity as an intellectual ideal, many of the debates that are explored reveal a degree of intellectual intolerance and this is refracted through the institutional system that structures marketing discourse.Originality/value– This account provides an introduction to the intellectual debates of the last century, highlighting the ebb and flow of marketing thought. It calls attention to debates that are largely under explored and highlights the politics of knowledge production in marketing and consumer research.
Mode of delivery and the probability of subsequent childbearing: a population‐based register study
Authors: Elvander C , Dahlberg J , Andersson G , Cnattingius S 
Published: August 2014

ObjectiveTo investigate the relationship between mode of first delivery and probability of subsequent childbearing.DesignPopulation‐based study.SettingNationwide study in Sweden.PopulationA cohort of 771 690 women who delivered their first singleton infant in Sweden between 1992 and 2010.MethodsUsing Cox's proportional‐hazards regression models, risks of subsequent childbearing were compared across four modes of delivery. Hazard ratios (HRs) were calculated, using 95% confidence intervals (95% CIs).Main outcome measuresProbability of having a second and third child; interpregnancy interval.ResultsCompared with women who had a spontaneous vaginal first delivery, women who delivered by vacuum extraction were less likely to have a second pregnancy (HR 0.96, 95% CI 0.95–0.97), and the probabilities of a second childbirth were substantially lower among women with a previous emergency caesarean section (HR 0.85, 95% CI 0.84–0.86) or an elective caesarean section (HR 0.82, 95% CI 0.80–0.83). There were no clinically important differences in the median time between first and second pregnancy by mode of first delivery. Compared with women younger than 30 years of age, older women were more negatively affected by a vacuum extraction with respect to the probability of having a second child. A primary vacuum extraction decreased the probability of having a third child by 4%, but having two consecutive vacuum extraction deliveries did not further alter the probability.ConclusionsA first delivery by vacuum extraction does not reduce the probability of subsequent childbearing to the same extent as a first delivery by emergency or elective caesarean section.