bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of temperature on microstructural evolution of solder alloys under thermomigration
Authors: Lin Tzy-Yang , Ouyang Fan-Yi
Published: February 2019

In this study, we report the effect of temperature on the microstructural evolution of flip chip solder joints under a temperature gradient of 2580 °C/cm at ambient temperatures of 100 °C, 125 °C, 150 °C, 160 °C, and 175 °C. The experimental results show that no microstructural evolution of un-stressed solders was found for samples tested at ambient temperatures of 100 °C and 125 °C, whereas thermomigration induced phase separation was observed for the samples tested at 150 °C, 160 °C, and 170 °C, suggesting that the thermomigration only occurred when the ambient temperature was higher than 150 °C. The theoretical derivation indicates that the threshold temperature difference needed to trigger thermomigration is found to be decreased with an increase in the ambient temperature. In addition, at a temperature gradient of 2580 °C/cm, the theoretical calculation indicated that a threshold temperature to trigger thermomigration is about 150 °C
Assortativity and mixing patterns in international supply chain networks
Authors: Piraveenan Mahendra , Senanayake Upul , Matous Petr , Todo Yasuyuki
Published: February 2019

As economic globalisation increases, inclination toward domestic protectionism is also increasing in many countries of the world. To improve the productivity and the resilience of national economies, it is important to understand the drivers and the barriers of the internatiolisation of economic activities. While internatiolisation of individual economic actors is difficult to explain using traditional theories, aggregate patterns may be explained to some extent. We take a network-centric perspective to describe the extent of corporate internatiolisation in different countries. Based on Newman’s assortativity coefficient, we design a range of assortativity metrics which are appropriate in the firm network context. Using these, we quantify companies’ appetite for internatiolisation in relation to the internatiolisation of their partners. We use the Factset Revere dataset, which is provided by FactSet Research Systems Inc., that captures global supply chain relationships between companies. We identify countries where the level of internationalisation is relatively high or relatively low, and we show that subtle differences in the assortativity metrics used change the ranking of countries significantly in terms of the assortativity correlation, highlighting that companies in different countries are prone to different types of internationalisation. Overall, we demonstrate that firms from most countries in the dataset studied have a slight preference to make supply chain relationships with other firms which have undergone a similar level of internationalisation, and other firms from their own country. The implications of our results are important for countries to understand the evolution of international relationships in their corporate environments, and how they compare to other nations in the world in this regard.
Development of a Rural Inter-professional Simulation Course: an initiative to improve trauma and emergency team management in New Zealand rural hospitals
Authors: Gutenstein Marc , Kiuru Sampsa , Withington Steve
Published: February 2019

ABSTRACT

BACKGROUND AND CONTEXT
New Zealand is a largely rural nation. Despite the regionalisation of trauma services, rural hospitals continue to provide trauma and emergency care. A dedicated rural inter-professional team-based simulation course was designed, as part of a wider strategy of using simulation-based education to address the disparity in experience and training for rural hospital teams providing emergency and trauma care.

ASSESSMENT
A pre-course questionnaire identified learning needs. Post-course evaluation and a follow-up survey assessed participants’ perception of the course, and whether lasting changes in clinical or organisational practice occurred.

RESULTS
Three courses were provided over 2 years to 60 interprofessional participants from eight rural hospitals. The course employed an interprofessional faculty and used skill workshops and high-fidelity trauma simulations to address learning needs identified in pre-course research. Evaluation showed the course to be an effective learning experience for participants. The post-course survey indicated possible lasting changes in team performance and rural hospital protocols. This educational strategy also allowed the collection of research data for investigating rural team dynamics and interprofessional learning.

STRATEGIES FOR IMPROVEMENT
Further development of rural interprofessional simulation courses should include more diverse clinical content, including paediatric and medical scenarios. Participant access was sometimes limited by typical rural challenges such as hospital staffing and locum availability.

LESSONS
Rural simulation-based education is both effective for rural trauma team training and a vehicle for rural research; however, there are challenges to participant access and course sustainability, which echo the rural–urban disparity.
Dominant aquatic species and their hydrological niches in freshwater ecosystems in a developing city
Authors: Yang S. , Pan T. , Wang X. , Sun Y. , Zhang Y. , Zhao C. , Gai Y. , Wang Z. , Zhang H.
Published: February 2019

Maintenance of appropriate hydrological niches is crucial to aquatic organisms. This study identified keystone species using the Ecopath with Ecosim food web model for hydrological niche analysis in Jinan City, the first pilot city of the Water Ecological Civilisation Project in China. The niche breadth of keystone species was analysed using Levins’ breadth model. Results revealed 35 keystone species in the aquatic ecosystems of Jinan City, including 5 phytoplankton, 7 zooplankton, 9 zoobenthos and 14 fish species. Streamflow was the most important hydrological factor affecting the phytoplankton, zooplankton, zoobenthos and fish communities in the study area, and excess variation in streamflow had an adverse effect on the normal evolution of the four biotic communities. We found that: (1) higher trophic levels in the food web contained more keystone species in the corresponding community; (2) carbon is an important element constraining the food web structure, and the magnitude of its effect on energy flow determines the degree of importance of the keystone species in the food web; and (3) changes to the survey season and at the spatiotemporal scale will have strong effects on the results of hydrological niche analysis and, to reduce these effects, it will be important to lengthen the spatial and temporal scales to cover both dry and flood seasons in the future. These results may provide an important basis for decision making regarding ecological scheduling and remediation of rivers in the study area, and potentially regions worldwide, thus facilitating aquatic ecological remediation and sustainable water resource management.
Generalizing the effects of chirality on block copolymer assembly
Authors: Wang Hsiao-Fang , Yang Kai-Chieh , Hsu Wen-Chun , Lee Jing-Yu , Hsu Jung-Tzu , Grason Gregory M. , Thomas Edwin L. , Tsai Jing-Cherng , Ho Rong-Ming
Published: February 2019

Significance

Chirality is a measure of asymmetry that is important in many branches of science. Homochiral evolution at different length scales is critical for molecular processes in nature (such as communication, replication, and enzyme catalysis) that rely on a delicate balance between molecular and conformational chirality and, most importantly, control the nature of the self-assembly of superstructures of constituent molecules. Here, we compare the homochiral evolution from molecular, to intrachain, to interchain, and, ultimately, to mesodomain chirality from the self-assembly of a pair of block copolymers possessing a chiral block that exhibits one of the two different stereochemistries. The comparison sheds light on the physical mechanisms that link chiral structure across these length scales in this prototypical class of self-assembling materials.
Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids
Authors: Zhuang Xuan , Yang Chun , Murphy Katherine R. , Cheng C.-H. Christina
Published: February 2019

A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of the
AFGP
genomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essential
cis
promoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadid
AFGP
originated from entirely nongenic DNA. The gadid
AFGP
evolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.
Microscopic description of acid–base equilibrium
Authors: Grifoni Emanuele , Piccini GiovanniMaria , Parrinello Michele
Published: February 2019

Significance

Acid–base reactions are among the most important chemical processes. Yet we lack a simple way of describing this class of reactions as a function of the atomic coordinates. In fact, once dissolved in water,

H

+

and its conjugate anion

OH

−

have a highly fluxional structure difficult to pin down. Here we solve this issue by taking the point of view of describing acid–base reactions as an equilibrium between the solute and the whole solvent. This allows identifying generally applicable descriptors. As a consequence it is now possible to perform quantitative enhanced sampling simulation of acid–base reaction in water and in other environments such as the zeolite cavities or at surfaces.
A humanitarian disaster or invasion of Europe?
Authors: Koca-Helvacı Zeynep Cihan
Published: February 2019

This study sought to find out how language resources were employed to reflect the changing media attitude towards immigrants during the 2015 Migrant Crisis. Combining relevant analytical categories of the Socio-Cognitive Approach (Van Dijk 1991), the Discourse-Historical Approach (Wodak 2001) and the Social Actor Analysis (van Leeuwen 2008) with Corpus Linguistic techniques, it compared the British media coverage of two critical cases; the Death of Aylan Kurdi, and the Cologne Sexual Assaults. The findings show that in both cases, regardless of news content, immigration was problematized as a crisis, controversy, and catastrophe. The scale of the tragedy and the possibility of an immigrant influx to the UK deeply influenced the media representation of the immigrants.
The great wall of Europe
Authors: Silaški Nadežda , Đurović Tatjana
Published: February 2019

Complementing the theoretical framework of Critical Metaphor Analysis (Charteris-Black 2004; Musolff 2004, 2011) with research on multimodality from a cognitive viewpoint (Bounegru and Forceville 2011), in this chapter we deal with both linguistic and multimodal instantiations of the wall metaphor in Serbian media texts published in 2015 in an attempt to identify the most frequent metaphor scenarios modelled around this concept in a critical period during the European migrant crisis. Two major metaphor scenarios (Musolff 2006) triggered by the wall metaphor arise – fortress europe and berlin wall, both appearing to be instrumental in communicating the notions of marginalisation and non-belongingness to the EU space, emanating from verbally and visually constructed image of both migrants and the Serbian nation.
Expressing ‘possession’
Authors: Aikhenvald Alexandra Y.
Published: February 2019

Competing motivations are often at work in the choice of form and meaning of possessive and associative noun phrases. The article offers a broad typological review of the ways of expressing possession at the NP-internal level. In particular, it discusses how iconicity and economic motivations interact in determining the shape of NP-internal possessive expressions, also addressing the topics of how socio-cultural factors affect the grammar of possession and how societal changes are reflected in language variation.
Predicative possession in South Saami
Authors: Inaba Nobufumi , Blokland Rogier
Published: February 2019

In this paper, we analyse and describe the HAVE-constructions in South Saami (Saamic, Uralic), from a comparative perspective with other Saamic and Uralic languages. The Saamic languages can be divided into three subgroups: in the first, HAVE is expressed with a verb meaning ‘to be’; the second has a HAVE-construction based on a verb ‘to have’ and one on the verb ‘to be’. The third subgroup comprises only of South Saami, which has three HAVE-constructions, one based on the verb ‘to have’ and two on the verb ‘to be’. South Saami is also unique among Saamic languages in that it has a HAVE-construction based on the verb ‘to be’ where the possessor in the genitive.
Predicative possession in North Saami and Norwegian
Authors: Mazzitelli Lidia Federica
Published: February 2019

This paper describes the strategies employed by North Saami (Uralic, Saamic) and Norwegian (Indo-European, North Germanic) to express predicative possession. It shows that both North Saami and Norwegian do not provide evidence of splits in their possession systems; rather, they use the same constructions to express both ownership as well as less prototypical possessive notions, displaying a typical European behaviour. The expression of some notions contiguous to possession, namely experience, location and attribution is also analyzed: these are rarely coded by means of possessive constructions in Norwegian, but more often in North Saami.
Superlative readings of possessive constructions in Turkic
Authors: Nevskaya Irina , Tazhibayeva Saule
Published: February 2019

The article describes the superlative, hyperlative and elative use of formally possessive constructions in a number of Turkic languages from a comparative perspective, analyzing their structural and semantic types and pragmatic properties. Similar possessive superlative constructions are found all over Eurasia in languages belonging to various language families: they mostly express abstract (absolute) comparison of referred entities where their quantities are compared with a certain norm. One of the most unclear issues of possessive superlative constructions is their origin. They could have emerged as structural copies of corresponding Semitic Biblical expressions or as effect of language internal developments. The material of corresponding English and German non-canonical possessive constructions allows assuming that both factors have contributed to their emergence.
Possession in Khinalug
Authors: Rind-Pawlowski Monika
Published: February 2019

The article describes the functions and the usage of the genitive in Khinalug, a Nakh-Dagestanian language spoken in the North-East of Azerbaijan. Khinalug stands out for its tripartite genitive system with two subsystems: (a) a possessee-based subsystem, which distinguishes alienability versus certain types of inalienability according to the degree of bondedness towards the possessee; only animate possessors can take an inalienably marked possessee. (b) a possessor-based subsystem, which distinguishes alienability versus family-relatedness according to the bondedness among the members of the possessor group towards each other: They have to be in a family relationship to justify the use of this genitive. Moreover, independently from animacy, the alienable and the inalienable genitive are governed by a range of postpositions.
Competing possessive constructions in Late Latin documents from Italy
Authors: Valentini Cecilia
Published: February 2019

This paper illustrates the grammaticalisation of the preposition de as a genitive marker through the analysis of Early Medieval notary deeds written in northern and central Italy (Codice diplomatico longobardo, CDL). In Classical Latin, de is used mainly as a verbal adjunct; its usage at the noun phrase level is sporadic and semantically determined, conveying mainly the meaning of ‘source’. By the time of the CDL documents, de has a more grammaticalised status and a higher frequency, but has not yet affected the expression of kinship and ownership. Semantic factors such as the prototypicality of the possessive relation and the degree of animacy of the modifier can motivate this concurrence between the synthetic and the analytical pattern of adnominal possession.
Grammatical relations in Mapudungun
Authors: Zúñiga Fernando
Published: February 2019

This article presents the grammatical relations (GRs) of Central Mapudungun (unclassified, Chile and Argentina) as explored in terms of argument selection as instantiated by different constructions (i.e., the coding and behavioral properties usually discussed in the literature on alignment). The language emerges as having an essentially head-marking clausal morphosyntax that contrasts “subjects”, primary and secondary “objects,” and adjuncts, with two important provisos. These GRs differ from the run-of-the-mill notions due to the difference between direct and inverse transitive clauses (which responds to a person- and topicality-based hierarchy of participants and allows for agentive or patientive subjects and patientive or agentive primary objects, respectively), and to some apparent heterogeneity shown across constructions by the two most prominent GRs.
Grammatical relations in Hiligaynon
Authors: Mithun Marianne
Published: February 2019

In typological work on grammatical relations, languages of the Philippines have long presented challenges. The challenges are due in part to differences across the languages, and in part to the nature of the data underlying analyses. Here the system is described for one Philippine language, Hiligaynon. Basic clause structures are described, then alternations involving causatives, applicatives, reflexives, middles, and reciprocals. Choices among these constructions are examined in context, revealing effects of referent properties (animacy, identifiability, specificity), and information flow through discourse (topicality, topic shifts, focus). Argument structure constraints on individual syntactic constructions are then detailed: imperatives, quantifier float, conjunction reduction, nominalization, content questions, relativization, secondary predication, and complementation. Examination of alternations in context allows us to refine existing typological generalizations and build new ones.
Grammatical relations in Basque
Authors: Zúñiga Fernando , Fernández Beatriz
Published: February 2019

This article presents the grammatical relations (GRs) of Standard Basque (isolate, Spain and France) as explored in terms of argument selection as instantiated by different constructions (i.e., the coding and behavioral properties usually discussed in the literature on alignment). The language emerges as showing comparatively simple dependent-marking patterns with quite intricate head-marking patterns (especially regarding morphological marking). These patterns combine accusative “deep syntax” with neutral “surface syntax” on the one hand, as well as coding patterns usually framed in terms of split ergativity (tam- and person-based) and split intransitivity (lexically based) on the other.
Grammatical relations in Balinese
Authors: Arka I Wayan
Published: February 2019

Grammatical relations in Balinese show good empirical evidence for the classification of syntactic dependents into core arguments, obliques and adjuncts. One of the core arguments is selected as Pivot, a well-defined syntactic notion with certain exclusive selectors, such as control and relativisation. The selectors distinguishing core arguments from obliques and adjuncts include phrasal flagging, fixed structural positioning, and possibility of quantifier float, depictive predicates, and argument elision in imperatives. Pivot selection and valence-changing operations, such as applicativisation, provide ample evidence for a symmetrical voice system, and clausal arguments which do not constitute a distinct grammatical relation. These properties, particularly that of passive-like voice alternation without demoting the actor argument to an oblique, pose a challenge in linguistic typology and linguistic theory.
Grammatical relations in Yakkha (Kiranti)
Authors: Schackow Diana
Published: February 2019

This article provides an analysis of the grammatical relations in Yakkha (Tibeto-Burman, Kiranti; Eastern Nepal). The study is based on the typological-theoretical framework established in Bickel (2011a) and Witzlack-Makarevich (2011). Yakkha does not have a dominant grammatical relation. It is rather a prime example for how diverse alignment patterns can be in a single language. The alignment patterns established by some argument selectors are role-based (i.e. accusative, ergative, etc.), while other argument selectors, particularly the verbal person marking, prefer reference-based selection principles. The verbal person marking is the core around which all morphosyntactic processes revolve. An intransitive and a transitive inflectional paradigms can be distinguished. Combined with different case marking options, several verb frames can be identified. Yakkha also has a number of operations affecting valency and transitivity. This article discusses the causative, the benefactive, the reflexive, the reciprocal, the middle, as well as the unmarked passive and antipassive. Yakkha also has a number of biclausal argument selectors: Whereas converbal clauses and participant nominalization show accusative alignment, relativization shows ergative alignment.
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data
Authors: Rashid Sabrina , Shah Sohrab , Bar-Joseph Ziv , Pandya Ravi
Published: February 2019

Motivation

Intra-tumor heterogeneity is one of the key confounding factors in deciphering tumor evolution. Malignant cells exhibit variations in their gene expression, copy numbers and mutation even when originating from a single progenitor cell. Single cell sequencing of tumor cells has recently emerged as a viable option for unmasking the underlying tumor heterogeneity. However, extracting features from single cell genomic data in order to infer their evolutionary trajectory remains computationally challenging due to the extremely noisy and sparse nature of the data.

Results

Here we describe ‘Dhaka’, a variational autoencoder method which transforms single cell genomic data to a reduced dimension feature space that is more efficient in differentiating between (hidden) tumor subpopulations. Our method is general and can be applied to several different types of genomic data including copy number variation from scDNA-Seq and gene expression from scRNA-Seq experiments. We tested the method on synthetic and six single cell cancer datasets where the number of cells ranges from 250 to 6000 for each sample. Analysis of the resulting feature space revealed subpopulations of cells and their marker genes. The features are also able to infer the lineage and/or differentiation trajectory between cells greatly improving upon prior methods suggested for feature extraction and dimensionality reduction of such data.

Availability and implementation

All the datasets used in the paper are publicly available and developed software package and supporting info is available on Github https://github.com/MicrosoftGenomics/Dhaka.

Supplementary information

Supplementary data are available at Bioinformatics online.
Ultrasonographic Evaluation of Gastric Contents in Term Pregnant Women Fasted for 6 Hours
Authors: Hakak S. , McCaul C.L. , Crowley L.
Published: February 2019

(Int J Obstet Anesth. 2018;34:15–20)

Fasting before elective anesthesia is intended to reduce gastric fluid volume and the risk of aspiration of gastric contents leading to aspiration pneumonitis, which can be life-threatening. Pregnant women are considered to be at increased risk of pulmonary aspiration due to some of the physiological changes of pregnancy, including relaxation of the lower esophageal sphincter and the upward displacement of the stomach by the gravid uterus. Current fasting guidelines vary among national anesthesiology organizations with most recommending at least 6 hours of fasting after a light meal and some suggesting 6 to 8 hours of fasting depending on the type of food consumed before anesthesia for elective procedures. This current prospective study was undertaken to analyze the stomach contents of nonlaboring term pregnant women after 6 hours of fasting, using ultrasonographic assessments.
Applying Surgical Antimicrobial Standards in Cesarean Deliveries
Authors: Fay K.E. , Yee L.
Published: February 2019

(Am J Obstet Gynecol. 2018;218(4):416.e1–416.e4)

Surgical site infections are costly and common in the United States. Most surgical guidelines for antimicrobial prophylaxis endorse repeat antibiotic administration after an estimated blood loss (EBL) of 1500 mL or following 1 to 2 half-lives of the agent. The American College of Obstetricians and Gynecologists have not made recommendations for redosing antibiotics in obstetric surgeries, and currently a single dose of preoperative antibiotics is considered standard of care. Parturients have increased renal clearance and may benefit from antimicrobial redosing.
Ethical Problems in Decision Making in the Neonatal ICU
Authors: Lantos J.D.
Published: February 2019

(N Engl J Med. 2018;379:1851–1860)

Disagreements regarding life-sustaining treatments in the neonatal intensive care unit (NICU) are not uncommon, especially when parental requests conflict with doctor recommendations. Cases that are intractable often end up in court, where outcomes can vary depending on state statutes. Ethicists have developed a general framework, first articulated in 1983, for balancing the child’s interest with the scope of parental authority. When benefits of treatment are clear, the baby’s right to treatment outweighs parental rights. When benefits of treatment are less clear, ethicists and courts often defer to parental choice. Nevertheless, gray zones still exist in conflict resolution. A new approach, emerging in the early 2000s, proposes that rather than only providing detailed, objective information, doctors help parents discern their own values and ethical commitments in these unanticipated situations. In this review, the author discussed this shift in approach and how advances in both prenatal diagnosis and neonatal therapeutics can change treatments and perspectives in the NICU.
A 36-Year-Old Pregnant Woman With Newly Diagnosed Adenocarcinoma
Authors: Murphy J.E. , Shampain K. , Riley L.E. , Clark J.W. , Basnet K.M.
Published: February 2019

(N Engl J Med. 2018;379:1562–1570)

A 36-year-old pregnant woman was evaluated at 33 weeks gestation because of newly diagnosed adenocarcinoma. At 32 weeks’ admission, the patient had presented to another hospital with a history of 3 days of nonradiating, severe pain accompanied by nausea in her lower back that rated 10 on a scale of 10 and originated in the epigastric region and migrated to the upper right quadrant and lower back. On examination, there was tenderness in the right upper quadrant. The gravid uterus was soft, and no abnormal fetal findings were observed. An incidental finding of renal ultrasonography showed the liver to be diffusely heterogenous and nodular, and to contain numerous masses. Abdominal magnetic resonance imaging without contrast revealed multiple lesions in the liver, some with central necrosis and with the largest being 7.4×3.9 cm. Computed tomography also revealed multiple hypoattenuating hepatic lesions, with the largest measuring 8.2 cm in diameter, with the presence of multiple enlarged periaortic and portocaval lymph nodes. Percutaneous liver biopsy revealed metastatic adenocarcinoma, poorly differentiated with widespread involvement of the liver and lymph nodes. Plans for chemotherapy and early fetal delivery were discussed with the patient, but at 32 weeks’ gestation, the patient left the first hospital because she thought her pain was undertreated and she and her spouse wanted to identify the primary cancer, understand treatment options, and obtain adequate pain relief. She presented to a second hospital at 33 weeks gestation, with continued ongoing severe back pain. No vaginal bleeding or contractions were found, and fetal movement was detectable in the gravid uterus.
Incidence and risk factors for iatrogenic distal tibia/fibula fracture during Ponseti technique of clubfoot treatment
Authors: Ranjan Rahul , Sud Alok , Adhikary Debashis , Sinha Abhinav , Chand Suresh
Published: February 2019

The incidence and risk factors of distal tibia/fibula fracture, an uncommon complication during Ponseti manipulation, are unknown. We evaluated 222 virgin clubfeet of patients aged less than 3 years for fractures of distal tibia/fibula. Incidence rate was found to be 1.3% per year. Associated risk factors were identified as neglected, syndromic clubfeet, feet requiring greater than 10 casts, post-tenotomy dorsiflexion less than 10° and casting by physician with less than 3 years of casting experience, with odds ratios of 14, 28, 4.9, 3.7 and 3.4, respectively. Most of these fractures healed without consequences; however, it is still advisable not to forcefully dorsiflex while casting, which may result in the fracture of distal tibia/fibula.
Anaplastic Lymphoma Kinase (ALK)-positive Tumors
Authors: Gupta Rohan , Amanam Idoroenyi , Rahmanuddin Syed , Mambetsariev Isa , Wang Yingyu , Huang Charity , Reckamp Karen , Vora Lalit , Salgia Ravi
Published: February 2019

Introduction:

Anaplastic lymphoma kinase (ALK)gene rearrangements are observed in about 4% to 8% non–small cell lung cancer (NSCLC).ALK+ tumors have been associated with increased pleural and pericardial disease. Our primary objective was to determine the uncommon sites of metastasis ofALK+ NSCLC. Secondary objectives included study of coexisting mutations and factors impacting survival ofALK+ NSCLC.

Methods:

All patients with metastaticALK+ NSCLC at the City of Hope Cancer Center in Duarte, California from 2010 to 2017 were selected for retrospective chart review. The demographic variables were collected. The molecular statuses of patients were evaluated through commercially available platforms for next-generation sequencing. Three-dimensional volumetric images were generated for the primary lesion and different sites of metastasis.

Results:

Sixty two patients withALK+ NSCLC were identified from 2010 to 2017. The median age was 59 with 36 (58%) female individuals and only 20 (32%) smokers. Twenty four patients had uncommon sites of metastasis which were thyroid, soft tissue, chest and abdominal wall, spleen, peritoneum, omentum, kidney, and ovary. Common characteristics of the primary lesions were right upper lobe location (N=23 [37%]), oval shape (N=22 [35%]), irregular margins (N=26 [42%]), solid lesions (N=27 [44%]), presence of pleural contact or effusion (N=22 [35%]). Twenty four patients had next-generation sequencing testing which showed coexisting mutations such asTP53(N=8),EGFR(N=5),KRAS(N=3). Patients with uncommon sites of metastasis had a decreased median survival compared with common sites (39 vs. 82 m,P=0.046).

Conclusion:

In NSCLC,ALKrearrangements may not be mutually exclusive mutations and can present with unique radiographic patterns. Patients with uncommon sites of metastasis may have worse outcomes.
Affective and Cognitive Attitudes on Cervical Health Behaviors Among Asian American Women
Authors: Lee Jongwon , Carvallo Mauricio , Lee Eunice , Chung Jane , Shin Chanam
Published: February 2019

Cervical cancer is a major cause of death for Vietnamese and Korean American women, yet their screening rates remain low. This study explored factors influencing cervical health behaviors of these populations, using a 2-dimensional model (ie, affect and cognition) of attitude structure approach. Semistructured interviews were conducted with 33 participants. A semantic content analysis was used to identify major codes and themes across the transcripts. Multiple aspects of both negative and positive affect and cognition, which led to 3 different cervical health behaviors (avoidance, ambivalence, and acceptance), emerged from the interviews. The clinical implications of these findings are discussed.
Food Security Status and Overweight/Obesity Among 2- to 5-Year-Old Boys and Girls in a Community-Based Clinic
Authors: Gipson-Jones Trina L. , O'Neal LaToya J. , Sheats Jylana L. , Thorpe Roland J. , Beech Bettina M. , Bruce Marino A.
Published: February 2019

The purpose of this study was to examine relationships between food security, parental health behaviors, and overweight/obesity among 2- to 5-year-old children in West Tennessee (N = 264). Results from logistic regression models indicate that the association between parental characteristics and child weight status varies by child sex and household food security. These findings highlight the need for more nuanced analysis that can produce results that inform and shape the development of precise health promotion and intervention strategies designed for diverse low-resource populations.
Early Routine Use of Upper GI Contrast Series Post Paraesophageal Hernia Repair: A Single Institution Consecutive Case Series
Authors: Robertson-More Connal , Prasad Shalvin , Gill Richdeep , Church Neal , Mitchell Philip , Debru Estifanos
Published: February 2019

Introduction:

There is conflicting evidence with regard to the routine use of upper gastrointestinal contrast series in detecting early complications post paraesophageal hernia repair (PEHR).

Methods:

All cases booked for a PEHR between January 2007 and September 2015 were identified using hospital records. Standard demographic, operation, and imaging data were extracted.

Results:

We retrospectively identified 391 PEHR cases between January 2007 and September 2015. The mean age at the index operation was 66.7 years with a female predominance. The majority of index operations were elective and completed for a large paraesophageal hernia. Contrast studies were reported as normal in 70.6%, a leak in 0.3%, an obstruction in 27.9%, and early recurrence in 1.0%. Reoperation was required in 1.8% of cases.

Conclusion:

Routine upper gastrointestinal contrast studies post-PEHR changed management in 0.8% of cases and were unhelpful in determining the need for early reoperation in 57.1% of cases requiring reoperation.
Pediatric blunt renal trauma practice management guidelines: Collaboration between the Eastern Association for the Surgery of Trauma and the Pediatric Trauma Society
Authors: Hagedorn Judith C. , Fox Nicole , Ellison Jonathan S. , Russell Robert , Witt Cordelie E. , Zeller Kristen , Ferrada Paula , Draus John M.
Published: February 2019

BACKGROUND

Injury to the kidney from either blunt or penetrating trauma is the most common urinary tract injury. Children are at higher risk of renal injury from blunt trauma than adults, but no pediatric renal trauma guidelines have been established. The authors reviewed the literature to guide clinicians in the appropriate methods of management of pediatric renal trauma.

METHODS

Grading of Recommendations Assessment, Development and Evaluation methodology was used to aid with the development of these evidence-based practice management guidelines. A systematic review of the literature including citations published between 1990 and 2016 was performed. Fifty-one articles were used to inform the statements presented in the guidelines. When possible, a meta-analysis with forest plots was created, and the evidence was graded.

RESULTS

When comparing nonoperative management versus operative management in hemodynamically stable pediatric patient with blunt renal trauma, evidence suggests that there is a reduced rate of renal loss and blood transfusion in patients managed nonoperatively. We found that in pediatric patients with high-grade American Association for the Surgery of Trauma grade III-V (AAST III-V) renal injuries and ongoing bleeding or delayed bleeding, angioembolization has a decreased rate of renal loss compared with surgical intervention. We found the rate of posttraumatic renal hypertension to be 4.2%.

CONCLUSION

Based on the completed meta-analyses and Grading of Recommendations Assessment, Development and Evaluation profile, we are making the following recommendations: (1) In pediatric patients with blunt renal trauma of all grades, we strongly recommend nonoperative management versus operative management in hemodynamically stable patients. (2) In hemodynamically stable pediatric patients with high-grade (AAST grade III-V) renal injuries, we strongly recommend angioembolization versus surgical intervention for ongoing or delayed bleeding. (3) In pediatric patients with renal trauma, we strongly recommend routine blood pressure checks to diagnose hypertension. This review of the literature reveals limitations and the need for additional research on diagnosis and management of pediatric renal trauma.

LEVEL OF EVIDENCE

Guidelines study, level III.
Non-motor effects of subthalamic nucleus stimulation in Parkinson’s patients
Authors: Sammartino Francesco , Marsh Rachel , Rezai Ali , Krishna Vibhor
Published: February 2019

Introduction

The existing white matter connectivity analyses of the subthalamic region have mainly included the motor effects of deep brain stimulation.

We investigate white matter connectivity associated with the stimulation-induced non-motor acute clinical effects in three domains: mood changes, dizziness and sweating.

Methods

Using whole brain probabilistic tractography and seeding from the volumes of tissue activation, connectivity maps were generated and statistically compared across patients. The cortical voxels associated with each non-motor domain were compared with stimulation-induced motor improvements in a multivariate model. The resulting voxels maps were thresholded for false discovery (FDR q<0.05) and clustered using a multimodal atlas. To understand the role of local pathways in the subthalamic region, a group level parcellation was performed for each non-motor domain.

Results

The non-motor effects are rarely observed during stimulation titration: from 1100 acute clinical effects, mood change was observed in 14, dizziness in 23, and sweating in 20. Distinct cortical clusters were associated with each domain, notably mood change was associated with voxels in salience network and dizziness with voxels in visual association cortex. The subthalamic parcellation yielded a medio-lateral gradient with motor parcel being lateral and the non-motor parcels being medial. We also observed an antero-posterior organization in the medial non-motor clusters with mood changes (anterior), dizziness and sweating (posterior).

Conclusion

We interpret these findings based on the literature and foresee these to be useful for shaping the electrical field with the imminent use of steerable DBS electrodes.
Ohana: detecting selection in multiple populations by modelling ancestral admixture components
Authors: Cheng Jade Yu , Racimo Fernando , Nielsen Rasmus
Published: February 2019

One of the most powerful and commonly used methods for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this paper, we present a new maximum likelihood method for finding regions under positive selection. The method is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. We evaluate the method using simulated data and compare it to related methods based on summary statistics. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, like immunity, fat distribution, food intake, vision and hair development.
ICONIC MANAKINS AND DESPICABLE GRACKLES: COMPARING BIRD-RELATED CULTURAL ECOSYSTEM SERVICES ACROSS BIRDWATCHERS, FARMERS, AND URBANITES IN NORTHWESTERN COSTA RICA
Authors: Echeverri Alejandra , Naidoo Robin , Karp Daniel S. , Chan Kai M.A. , Zhao Jiaying
Published: February 2019

Despite the great cultural and economic benefits associated with birdwatching and other bird-related cultural ecosystem services (CES), little is known about the bird-related CES perceived by people, and how they differ across stakeholder groups and species. The goal of this study was to explore CES across three stakeholder groups in northwestern Costa Rica. We conducted surveys (n=404 total) in which we presented farmers (n=140), urbanites (n=149), and birdwatchers (n=115) with pictures and songs of bird species and collected participants’ ratings on items designed to measure multiple CES. We found bird-related CES were perceived as six different constructs: identity, bequest, education, birdwatching, acoustic aesthetic, and disservices. The three stakeholder groups varied across these constructs and across species. Specifically, birdwatchers ranked species higher in terms of their education scores and lower in disservices scores compared to the other two groups. Positive correlations across CES, and negative correlations with disservices, suggest that the affect heuristic (by which generalized positive or negative feelings sway judgements of risks and benefits) might be informing bird-related CES. Our approach represents a novel method for assessing CES that can be adapted and modified for different taxa and multiple geographical contexts.
Bayesian abundance estimation from genetic mark-recapture data when not all sites are sampled: an example with the bowhead whale
Authors: Frasier Timothy R. , Petersen Stephen D. , Postma Lianne , Johnson Lucy , Heide-Jørgensen Mads Peter , Ferguson Steven H.
Published: February 2019

Estimating abundance is one of the most fundamental and important aspects of population biology, with major implications on how the status of a population is perceived and thus on conservation and management efforts. Although typically based on one of two methods (distance sampling or mark-recapture), there are many individual identification methods that can be used for mark-recapture purposes. In recent years, the use of genetic data for individual identification and abundance estimation through mark-recapture analyses have increased, and in some situations such genetic identifications are more efficient than their field-based counterparts for population monitoring. One issue with mark-recapture analyses, regardless of which method of individual identification is used, is that the study area must provide adequate opportunities for “capturing” all individuals within a population. However, many populations are unevenly and widely distributed, making it unfeasible to adequately sample all necessary areas. Here we develop an analytical technique that accounts for unsampled locations, and provides a means to infer “missing” individuals from unsampled locations, and therefore obtain more accurate abundance estimates when it is not possible to sample all sites. This method is validated using simulations, and is used to estimate abundance of the Eastern Canada-West Greenland (EC-WG) bowhead whale population. Based on these analyses, the estimated size of this population is 9,089 individuals, with a 95% highest density interval of 5,107–17,079.
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation
Authors: Lhoumaud Priscillia , Sethia Gunjan , Izzo Franco , Badri Sana , Cornwell MacIntosh , Kim Kyu-Tae , Landau Dan Avi , Skok Jane
Published: February 2019

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a low input, low sequencing depth method, EpiMethylTag that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA.
Terahertz Circular Dichroism Spectroscopy of Biomaterials Enabled by Kirigami Polarization Modulators
Authors: Choi Won Jin , Cheng Gong , Huang Zhengyu , Zhang Shuai , Norris Theodore B. , Kotov Nicholas A.
Published: February 2019

ABSTRACTS

Terahertz circular dichroism (TCD) offers spectroscopic capabilities for understanding mesoscale chiral architecture and low-energy vibrations of macromolecules in (bio)materials1–5. However, the lack of dynamic polarization modulators comparable to polarization optics for other parts of electromagnetic spectrum impedes proliferation of TCD spectroscopy6–10. Here we show that tunable optical elements fabricated from patterned plasmonic sheets with periodic kirigami cuts make possible polarization modulation of THz radiation under application of mechanical strain. A herringbone pattern of microscale metal stripes enables dynamic range of polarization rotation modulation exceeding 80° over thousands of cycles. Upon out-of-plane buckling, the plasmonic stripes function as reconfigurable semi-helices of variable pitch aligned along the THz propagation direction. Several biomaterials, exemplified by elytrons of Chrysina gloriosa beetles, revealed distinct TCD fingerprints associated with the helical substructure in the biocomposite. Analogous kirigami modulators will also enable other applications in THz optics, such as polarization-based terahertz imaging and phase-encrypted telecommunication.