bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond “not undermining”: possibilities for global cooperation to improve environmental protection in areas beyond national jurisdiction
Authors: Friedman Andrew 
Published: November 2018

Abstract
States have committed to “not undermine” relevant existing legal instruments, bodies, and frameworks in their negotiations over a new, legally binding instrument concerning biodiversity in areas beyond national jurisdiction (ABNJ). An agreed interpretation of “not undermine” will most likely be expressed through the institutional model adopted by this new instrument. Potential models should be evaluated in light of limitations on existing regional and sectoral ocean governance organizations, which may suggest governance gaps that the new instrument may fill. This article revisits the textual analysis of “not undermine” undertaken by Scanlon (2018) to explore its implications for the institutional models available to the new instrument. It reviews the practice of regional fishery management organizations as presented by Scanlon to identify areas where the new instrument might address persistent challenges. Finally, it suggests several potential models for the new instrument that might avoid “undermining” whereas improving governance outcomes in ABNJ. It concludes that a global institution with consultative links to existing organizations may provide the most logical means of implementation.
Multisite and multishift personnel planning with set-up costs
Authors: Nearchou A C , Giannikos I C , Lagodimos A G 
Published: November 2018

Abstract
Consideration is given to a personnel planning problem occurring in multisite projects. In this problem a set of facilities (different sites) need to complete a given work load over a planning horizon of several days. The workforce is skilled and can work on any facility and it is employed to work on a basis of workday shifts. A fixed set-up cost associated with each facility is incurred each time a facility starts operating. The problem seeks to determine when each facility should be operated as well as the manpower needed at each shift to complete the workload targets of all the facilities within the planning horizon at a minimum cost. First, a formulation of the new problem as a mixed-integer linear programme is given. Then, since the problem is shown to be NP-hard, a novel genetic algorithm (GA) is presented for its solution which incorporates a problem-specific coding together with new special merging rules for creating offspring that exploits the structure of the problem. Using results from the standard CPLEX optimizer we test the performance of the GA for a variety of operating environments. The results demonstrate very satisfactory performance for the GA in terms of both solution time and quality.
Keyhole, Trans-Sylvian, Trans-Sulcal Resection of an Insular Cerebral Cavernous Malformation: 2-Dimensional Operative Video
Authors: Norat Pedro , Yagmurlu Kaan , Park Min S , Kalani M Yashar S 
Published: November 2018

Abstract
Microsurgical resection of deep-seated cerebral cavernous malformations may result in a high rate of temporary and a lower, but nonetheless significant, rate of permanent disability. Use of trans-sulcal corridors may allow the surgeon to gain access to select deep-seated lesions without injury. Informed consent was obtained from this patient for a minimally invasive trans-sulcal approach to the malformation. This video illustrates the use of a trans-Sylvian, trans-sulcal approach to resect a deep insular/basal ganglia cavernous malformation in a young patient. The use of the neuronavigation is essential for success in these types of operation as this tool limits the surgeon's footprint in eloquent brain. Unlike superficial lesions where the removal of hemosiderin stained brain is possible and often safe, resection of deep-seated lesions requires the surgeon to distinguish between hemosiderin-stained brain and residual cavernous malformation. This task is not simple, and residual cavernous malformation is the most common reason for re-bleed in patients who have undergone surgery. Resection of symptomatic cavernous malformations in deep locations can be performed safely, but outcomes are heavily influenced by proper patient selection and surgeon experience. In patients with multiple cerebral cavernous malformations, such as the one in this case, genetic testing should be performed.
The Supra/Infra Transtentorial Transfalcine Approach for the Removal of a Falcotentorial Meningioma: 2-Dimensional Video
Authors: Mendez-Rosito Diego 
Published: November 2018

Abstract
Falcotentorial meningiomas originate in the junction of the falx cerebri and the tentorium. Due to its anatomic vicinity, these tumors have a close relationship with important neurovascular structures surrounding the pineal region including the deep venous system. Surgical approaches would normally consider posterior midline corridors, but decision between supra or infratentorial access should be considered by the size, anatomic displacement of structures, and the infiltration of the dural attachment.
This surgical video
1,2
demonstrates the surgical technique and pearls to achieve a stepwise resection of a complex falcotentorial meningioma. We present a case of a 42-yr-old female patient, neurologically intact at presentation. A semi-sitting position was used. Appropriate management of cerebrospinal fluid was obtained with an external ventricular drainage which is kept closed until the dura is opened. A suprainfratentorial craniotomy was done with adequate exposure of the superior sagittal sinus and torcula. The supracerebellar infratentorial corridor was used for inferior internal debulking and arachnoidal dissection of the tumor while the exposure obtained in the posterior interhemispheric allowed a corridor which exposed widely the tumor with transtentorial transfalcine extension. Adequate management of adjacent structures was done while preserving the straight sinus and vein of Galen. A gross total removal of the tumor was achieved and the patient was discharged without complications.
After this surgical video, the viewer will have learned the steps to safely achieve a surgical removal of a falcotentorial meningioma taking care of its relationship with the venous and neural adjacent structures.
The Effect of Electric Stimulation Techniques on Pain and Tenderness at the Myofascial Trigger Point: A Systematic Review
Authors: Ahmed Sara , Haddad Christopher , Subramaniam Shoba , Khattab Shereen , Kumbhare Dinesh 
Published: November 2018

AbstractBackgroundMyofascial pain is a prevalent chronic pain disorder, affecting a large proportion of the general population. Electric stimulation techniques such as transcutaneous electric stimulation (TENS) and electroacupuncture have been shown to be effective for managing chronic pain conditions including myofascial pain. The goal of this study was to review the literature on the effectiveness of electric stimulation techniques on myofascial pain.MethodsA comprehensive systematic search of three databases—Medline, EMBASE, and Cochrane CENTRAL—was conducted using key words related to myofascial pain and trigger points, as well as various electric stimulation techniques. A total of 15 articles passed the inclusion and exclusion criteria for the study. Data were extracted from these studies and assessed qualitatively and quantitatively. Standardized mean differences (SMDs) were computed from pain intensity measures extracted from these studies. Subgroup analyses were performed to assess the effectiveness of treatment modality, number of treatment sessions, frequency of stimulation, location of treatment, and duration of treatment.ResultsThe SMD for electric stimulation techniques on reported pain intensity was significant (P = 0.03), as was the SMD for the electroacupuncture subgroup (P = 0.02); the TENS subgroups’ effect was not significant (P = 0.17). The subgroup analyses tentatively suggest that frequency and number of treatments do not influence pain intensity, whereas the duration of treatment may have an effect. The qualitative results of this study revealed variability in the results among studies delivering TENS treatments.ConclusionsElectric stimulation is effective at mitigating reported pain intensity at the location of the trigger point. Electroacupuncture presented with significant and larger effect sizes of improvement relative to TENS for reported pain intensity. Given that this review included a small number of studies, there is a need for additional research to confirm its findings. Additionally, studies assessing the parameters and physiological location of treatment are needed to inform the clinical use and recommendations of electric stimulation treatments.
Neural Basis of the Sound-Symbolic Crossmodal Correspondence Between Auditory Pseudowords and Visual Shapes
Authors: McCormick Kelly , Lacey Simon , Stilla Randall , Nygaard Lynne C. , Sathian K. 
Published: November 2018

ABSTRACTSound symbolism refers to the association between the sounds of words and their meanings, often studied using the crossmodal correspondence between auditory pseudowords, e.g. ‘takete’ or ‘maluma’, and pointed or rounded visual shapes, respectively. In a functional magnetic resonance imaging study, participants were presented with pseudoword-shape pairs that were sound-symbolically congruent or incongruent. We found no significant congruency effects in the blood oxygenation level-dependent (BOLD) signal when participants were attending to visual shapes. During attention to auditory pseudowords, however, we observed greater BOLD activity for incongruent compared to congruent audiovisual pairs bilaterally in the intraparietal sulcus and supramarginal gyrus, and in the left middle frontal gyrus. We compared this activity to independent functional contrasts designed to test competing explanations of sound symbolism, but found no evidence for mediation via language, and only limited evidence for accounts based on multisensory integration and a general magnitude system. Instead, we suggest that the observed incongruency effects are likely to reflect phonological processing and/or multisensory attention. These findings advance our understanding of sound-to-meaning mapping in the brain.
The pentaglycine bridges ofStaphylococcus aureuspeptidoglycan are essential for cell integrity
Authors: Monteiro João M. , Münch Daniela , Filipe Sérgio R. , Schneider Tanja , Sahl Hans-Georg , Pinho Mariana G. 
Published: November 2018

AbstractBacterial cells are surrounded by cell wall, whose main component is peptidoglycan (PG), a macromolecule that withstands the internal turgor of the cell. PG composition can vary considerably between species. The Gram-positive pathogenStaphylococcus aureuspossesses highly crosslinked PG due to the presence of cross bridges containing five glycines, which are synthesised by the FemXAB protein family. FemX adds the first glycine of the cross bridge, while FemA and FemB add the second and the third, and the fourth and the fifth glycines, respectively. Of these, FemX was reported to be essential. To investigate the essentiality of FemAB, we constructed a conditionalS. aureusmutant of thefemABoperon. Depletion offemABwas lethal, with cells appearing as pseudomulticellular forms that eventually lyse due to extensive membrane rupture. This deleterious effect was mitigated by drastically increasing the osmolarity of the medium, indicating that pentaglycine crosslinks are required forS. aureuscells to withstand internal turgor. Despite the absence of canonical membrane targeting domains, FemA has been shown to localise at the membrane. To study its mechanism of localisation, we constructed mutants in key residues present in the putative transferase pocket and the α6 helix of FemA, possibly involved in tRNA binding. Mutations in the α6 helix led to a sharp decrease in protein activityin vivoandin vitrobut did not impair correct membrane localisation, indicating that FemA activity is not required for localisation. Our data indicates that, contrarily to what was previously thought,S. aureuscells do not survive in the absence of a pentaglycine cross bridge.
Identification of community-consensus clinically relevant variants and development of single molecule molecular inversion probes using the CIViC database
Authors: Barnell Erica K. , Waalkes Adam , Penewit Kelsi , Campbell Katie M. , Skidmore Zachary L. , Pritchard Colin C. , Fehniger Todd A. , Uppaluri Ravindra , Govindan Ramaswamy , Griffith Malachi , Salipante Stephen J. , Griffith Obi L. 
Published: November 2018

AbstractClinical targeted sequencing panels are important for identifying actionable variants for cancer patients, however, there are currently no strategies to create impartial and rationally-designed panels to accommodate rapidly growing knowledge within the field. Here we use the Clinical Interpretations of Variants in Cancer database (CIViC) in conjunction with single-molecule molecular inversion probe (smMIP) capture to identify and design probes targeting clinically relevant variants in cancer. In total, 2,027 smMIPs were designed to target 111 eligible CIViC variants. The total genomic region covered by the CIViC smMIPs reagent was 61.5 kb. When compared to existing genome or exome sequencing results (n = 27 cancer samples from 5 tumor types), CIViC smMIP sequencing demonstrated a 95% sensitivity for variant detection (n = 61/64 variants). Variant allele frequency for variants identified on both sequencing platforms were highly concordant (Pearson correlation = 0.885; n = 61 variants). Moreover, for individuals with paired tumor/normal samples (n = 12), 182 clinically relevant variants missed by original sequencing were discovered by CIViC smMIPs sequencing. This design paradigm demonstrates the utility of an open-sourced database built on attendant community contributions for each variant with peer-reviewed interpretations. Use of a public repository for variant identification, probe development, and variant annotation could provide a transparent approach to build a dynamic next-generation sequencing–based oncology panel.
Comparative study of population genomic approaches for mapping colony-level traits
Authors: Inbar Shani , Cohen Pnina , Yahav Tal , Privman Eyal 
Published: November 2018

AbstractSocial insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are the sum of individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction and sequencing for genome wide association (GWAS) studies of colony-level traits. We evaluate the accuracy of allele frequency estimation in sequencing a pool of individuals (pool-seq) from each colony in either whole-genome sequencing or reduced representation genomic sequencing. Based on empirical measurement of the experimental noise in sequencing DNA pools, we show that whole-genome pool-seq is more accurate than reduced representation pool-seq. We evaluate the power of the alternative approaches for detecting quantitative trait loci (QTL) of colony-level traits by using simulations that account for an environmental effect on the phenotype. Our results can inform experimental designs and enable optimizing the power of GWAS depending on budget, availability of samples and research goals. We conclude that for a given budget, sequencing un-normalized pools of individuals from each colony achieves greater QTL detection power.
Universal architectural concepts underlying protein folding patterns
Authors: Lesk Arthur M. , Subramanian Ramanan , Allison Lloyd , Abramson David , Stuckey Peter J. , Banda Maria Garcia de la , Konagurthu Arun S. 
Published: November 2018

ABSTRACTWhat is the architectural ‘basis set’ of the observed universe of protein structures? Using information-theoretic inference, we answer this question with a comprehensive dictionary of 1,493 substructuralconcepts. Eachconceptrepresents a topologically-conserved assembly of helices and strands that make contact. Any protein structure can be dissected into instances of concepts from this dictionary. We dissected the world-wide protein data bank and completely inventoried all concept instances. This yields an unprecedented source of biological insights. These include: correlations between concepts and catalytic activities or binding sites, useful for rational drug design; local amino-acid sequence–structure correlations, useful forab initiostructure prediction methods; and information supporting the recognition and exploration of evolutionary relationships, useful for structural studies. An interactive site, Proçodic, athttp://lcb.infotech.monash.edu.au/prosodic(click) provides access to and navigation of the entire dictionary of concepts, and all associated information.
Structural basis for ion selectivity in TMEM175 K+ channels
Authors: Brunner Janine D. , Jakob Roman P. , Schulze Tobias , Neldner Yvonne , Moroni Anna , Thiel Gerhard , Maier Timm , Schenck Stephan 
Published: November 2018

AbstractThe TMEM175 family constitutes recently discovered K+ channels that lack signatures for a P-loop selectivity filter, a hallmark of all known K+ channels. This raises the question how selectivity in TMEM175 channels is achieved. Here we report the X-ray structure of a bacterial TMEM175 family member in complex with a novel chaperone built of a nanobody fusion-protein. The structure of the channel in a non-conductive conformation was solved at 2.4 Å and revealed bound K+ ions along the channel pore. A hydrated K+ ion at the extracellular pore entrance that could be substituted with Cs+ and Rb+ is coordinated by backbone-oxygens forming a cation-selective filter at the tip of the pore-lining helices. Another K+ ion within the pore indicates the passage of dehydrated ions. Unexpectedly, a highly conserved threonine residue deeper in the pore conveys the K+ selectivity. The position of this threonine in the non-conductive state suggests major conformational rearrangements of the pore-lining helices for channel opening, possibly involving iris-like motions.
Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
Authors: Chen Wei , McKenna Aaron , Schreiber Jacob , Yin Yi , Agarwal Vikram , Noble William Stafford , Shendure Jay 
Published: November 2018

AbstractNon-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error patterns of NHEJ are strongly biased by sequence context, but these studies were based on relatively few templates. To investigate this more thoroughly, we systematically profiled ∼1.16 million independent mutational events resulting from CRISPR/Cas9-mediated cleavage and NHEJ-mediated DSB repair of 6,872 synthetic target sequences, introduced into a human cell line via lentiviral infection. We find that: 1) insertions are dominated by 1 bp events templated by sequence immediately upstream of the cleavage site, 2) deletions are predominantly associated with microhomology, and 3) targets exhibit variable but reproducible diversity with respect to the number and relative frequency of the mutational outcomes to which they give rise. From these data, we trained a model that uses local sequence context to predict the distribution of mutational outcomes. Exploiting the bias of NHEJ outcomes towards microhomology mediated events, we demonstrate the programming of deletion patterns by introducing microhomology to specific locations in the vicinity of the DSB site. We anticipate that our results will inform investigations of DSB repair mechanisms as well as the design of CRISPR/Cas9 experiments for diverse applications including genome-wide screens, gene therapy, lineage tracing and molecular recording.
Effect of partial substitution of rice with sorghum and inclusion of hydrolyzable tannins on digestibility and postprandial glycemia in adult dogs
Authors: Teixeira Liege , Dourado Pinto Caroline Fredrich , Mello Kessler Alexandre de , Trevizan Luciano 
Published: November 2018

AbstractSorghum is used as a substitute of rice in dog food, owing to its nutritional similarity and low cost. However, its use has been associated with negative effects, like a reduction in palatability, digestibility, and enzyme activity, which can decrease nutrient absorption. The presence of condensed tannins (CT) in sorghum may cause these effects. Another tannin group, the hydrolysable tannins (HT), is known for its antioxidant properties. Research has shown the nutritional effects of sorghum on dogs, but the effect of HT on dogs remains unknown. We evaluated the effects of substituting rice with sorghum containing CT and inclusion of commercial extract of HT on digestibility, fecal and urinary characteristics, and postprandial blood glucose levels in adult dogs. Nine adult Beagle were randomly subjected to 4 treatments: 50% rice; (RS) 25% rice + 25% sorghum; (RHT) 50% rice + 0.10% HT; (RSHT) 25% rice + 25% sorghum + 0,10% HT. Tannins did not affect food intake. The digestibility of dry matter, organic matter, crude protein, acid hydrolyzed fat, gross energy, and metabolizable energy (ME) decreased with sorghum inclusion (P < 0.05). Sorghum also decreased protein digestibility (P < 0.05). Greater fecal dry matter was observed with the RHT diet. HT associated with sorghum reduced ME (P < 0.05). Sorghum inclusion enhanced fecal output, without altering fecal score (P > 0.05). No alterations in urinary characteristics were observed. Sorghum and HT did not affect the postprandial blood glucose response measured by the area under the curve (P > 0.05). The substitution of rice by sorghum negatively affected protein absorption and ME of the diets. Sorghum can be considered as a good source of carbohydrates in therapeutic diets for weight control. HT may potentiate the effect of CT, but more research is needed to evaluate its potential use in dog nutrition.
Country institutional profiles: evidence from Colombian software exporters
Authors: Torkkeli Lasse , Fuerst Sascha 
Published: November 2018

PurposeThe purpose of this paper is to illustrate how the perceived institutional environment of Colombian internationally operating small- and medium-sized enterprises (SMEs) in the software industry comes to determine their performance.Design/methodology/approachThe research applies regression modelling to a sample of 43 internationally operating Colombian SMEs in the software development industry, collected via an online survey.FindingsThe results indicate that the normative dimension of the institutional environment comes to determine the export performance of the SMEs. Conversely, the cognitive and regulatory dimensions of the institutional forces do not have a significant effect.Research limitations/implicationsThe cross-sectional nature of the survey tool, the single industry and the single country context place limitations on the generalisability of the results across different industry and country contexts.Practical implicationsThe results highlight the need for entrepreneurship-friendly norms and values in the context of internationalising SMEs in Latin America. Governments should focus on the development and promotion of international entrepreneurs that inspire and serve as role models for other entrepreneurs rather than concentrate on the creation of regulatory frameworks and the provision of knowledge of how to start and manage risk for the internationalising SME.Originality/valueThe study is one of the first to apply the Busenitzet al.(2000) scale on the institutional country profile to real entrepreneurs. Previous studies have mainly applied the framework to a sample of students or officers assigned to US embassies. Besides Renkoet al.’s (2009) conference paper, ours is the first one that links the country institutional profile to the performance of internationalising software firms and, especially, in the context of a Latin American country. The study, therefore, attempts to contribute to a better understanding of how a country’s institutional environment impacts the performance of internationalising SMEs.