bluuebunny/crossref_metadata_2025 huggingface dataset:
Flow through polydisperse pores in an anodic alumina membrane: A new method to measure the mean pore diameter
Authors: Kostaras Christos , Dellis Spilios , Christoulaki Anastasia , Anastassopoulos Dimitrios L. , Spiliopoulos Nikolaos , Vradis Alexandros , Toprakcioglu Chris , Priftis George D.
Published: November 2018

We describe a novel technique for the characterization of the mean pore radius of self-ordered porous anodic alumina membranes. We have studied the flow of liquids through cylindrical membrane pores under conditions of very low Reynolds number (Re ≪ 1). We find that the flow data are well-described by Poiseuille's law. Characterization is achieved through the application of the Hägen-Poiseuille equation on flow measurements conducted in a simple and compact experimental setup. This setup allows for the monitoring of flow as a result of the pressure difference between the two sides of the membrane without the use of sophisticated and costly laboratory equipment. The proposed method has been tested by flow experiments using liquids of various viscosities. Good agreement is found between the results obtained from the flow data and the pore radii measured by scanning electron microscopy. Consistent results for the mean pore radius for the same membrane have been obtained in all cases.
Strategies to facilitate the formation of free standing MoS2 nanolayers on SiO2 surface by atomic layer deposition: A DFT study
Authors: Shirazi M. , Kessels W. M. M. , Bol A. A.
Published: November 2018

In this study, we employ density functional theory calculations to investigate the very initial formation of a buffer layer during atomic layer deposition of MoS2 at the SiO2 (001) surface. In our previous study, we described that the self-limiting atomic layer deposition (ALD) reactions using Mo(NMe2)2(NtBu)2 as precursor and H2S as co-reagent terminate in the formation of a so-called building block on the SiO2 (001) surface. This building block consists of Mo which shares bonds with the surface O of SiO2 (001) at the bottom and terminal S at the top. Electronic band structure calculations indicate that the subsequently deposited buffer-layer that is composed of these building blocks has (opto)-electrical properties that are far from the ideal situation. Based on our studies, we propose alternative ALD chemistries which lead to the formation of a so-called underpinned building block. In this cluster, the Mo atoms are underpinned by S atoms, suppressing the formation of a buffer layer. This ultimately facilitates the formation of a free standing conformal 2D-MoS2 nanolayer at the interface. Through the proposed chemistries, the opto-electrical properties of the deposited layers will be preserved.
Integrative taxonomic methods reveal an incorrect synonymisation of the South African Pseudonereis podocirra (Schmarda) as the widespread Pseudonereis variegata (Grube) from Chile
Authors: Kara Jyothi , Macdonald Angus H. H. , Simon Carol A.
Published: November 2018

The nereidid Pseudonereis variegata (Grube, 1866) described from Chile includes 14 synonymised species from 10 type localities with a discontinuous distribution, but no taxonomic or molecular studies have investigated the status of this species outside Chile. Two synonymised species, Mastigonereis podocirra Schmarda, 1861 and Nereis (Nereilepas) stimpsonis Grube, 1866, were described from South Africa and investigated here using morphological examination. MtCOI species delimitation analyses and morphology were used to determine the status of P. variegata in South Africa. Morphological examination revealed that museum and freshly collected specimens from South Africa that conform to the general description of P. variegata are similar to M. podocirra and N. stimpsonis with respect to the consistent absence of homogomph spinigers in the inferior neuropodial fascicle, expanded notopodial ligules and the subterminal attachment of dorsal cirri in posterior parapodia. The synonymy of M. podocirra and N. stimpsonis as P. variegata are rejected and P. podocirra, comb. nov. is reinstated. Morphologically, Pseudonereis podocirra differed from specimens from Chile with regard to the numbers of paragnaths, the absence of homogomph spinigers and changes in parapodial morphology along the body. Independence of these species was further supported by genetic distances, automatic barcode gap discovery and multi-rate Poisson tree process species delimitation analyses of 77 mtCOI sequences. Haplotype network revealed no genetic structuring within the South African populations. http://zoobank.org/urn:lsid:zoobank.org:pub:F0B1A5AF-9CE9-4A43-ACCF-17117E1C2F21
Towards a constructional analysis of the progressive aspect in Texas German
Authors: Blevins Margaret
Published: November 2018

This paper provides a constructional analysis of progressive aspect in Texas German (TxG) in present, indicative, active, non-negative sentences. TxG speakers used the present tense (progressive), am-progressive, tun-progressive, and the adverb jetzt to translate English sentences containing the present tense progressive be + -ing into TxG. This paper compares translation elicitation data from TxG speakers from Gillespie County from Gilbert’s (1972)

Linguistic Atlas of Texas German, Guion (1996), and the present-day Texas German Dialect Project. It demonstrates that there is still a range of constructions available to TxGs to express progressivity, with the present tense being the most commonly used construction, followed by the temporal adverb jetzt (38%), the am-progressive (7%), and the tun-progressive (4%).
Texas German and English word order constructions in contact
Authors: Dux Ryan
Published: November 2018

After reviewing previous accounts of Texas German (TxG) syntax, I define the basic word order constructions of English and German and identify which are identical across the languages (i.e. diaconstructions). Next, I analyze 300 TxG utterances and determine whether their syntax corresponds more closely to German, English, or German-English diaconstructions. Finally, I discuss sentences exhibiting unusual word order and how they demonstrate the need for a (Diasystematic) Construction Grammar approach.
Displaced modification
Authors: Kishimoto Hideki , Hook Peter Edwin , Pardeshi Prashant
Published: November 2018

The picture-noun construction in Marathi has a constituent structure in which the imagee-NP marked with genitive case appears outside the participial complement clause, i.e. it does not appear as a direct argument to the verb in the complement clause. It is shown that Japanese has the same type of picture-noun construction, which is not an instance of the genitive-subject construction derived by nominative-genitive conversion. In the picture-noun construction, the genitive NP, which is structurally related to the picture noun head, is interpreted as the subject of the complement clause. We argue that the imagee NP controls an invisible pronoun residing in the complement clause, and is thus understood as the subject of that clause. We discuss a number of empirical facts regarding the picture-noun complements in Marathi and Japanese that provide support for this analysis.
On the distribution of the discourse particles -yo in Korean and -ne in Japanese
Authors: Yim Changguk , Dobashi Yoshihito
Published: November 2018

The purpose of this paper is to provide a preliminary comparative study of the discourse particles -yo in Korean and -ne in Japanese, both of which show up fairly ubiquitously in sentence-medial positions. They appear to have very similar distributions, but a closer look at them reveals that they are systematically different. Elaborating on Yim and Dobashi’s (2015, 2016) prosodic analysis of -yo in Korean, we give a novel account of the distributional differences between -yo and -ne. We propose that -yo and -ne are attached to a phonological phrase and a prosodic word, respectively, in the course of syntax-phonology mapping that proceeds derivationally, and that they are realized as intonational phrases as a result of this derivational procedure.
The role of perceived similarity and contrast
Authors: Hwang Hyun Kyung
Published: November 2018

This study explores a pattern of speech perception in Korean and Japanese with special attention to American English vowel /æ/. Two identification tests reveal that Korean speakers pay more attention to the second formant (F2) signaling the backness of a vowel, whereas Japanese speakers are more sensitive to the first formant (F1) signaling the height of a vowel. The distinct sensitivity to different acoustic cues in the languages discussed here is accounted for by two language-specific factors: Different L1 vowel systems and language-specific variations.
Favorable processing conditions in the production of passive sentences by Brazilian Portuguese-speaking children
Authors: de Lima Júnior João Claudio , Sicuro Corrêa Letícia M. , Augusto Marina Rosa Ana
Published: November 2018

This study focuses on the production of passives by children (3–4 and 5–6 years old) under favorable conditions. An experiment is reported in which passives were elicited by priming in a Snap Game, where a central character was the patient of the events depicted in the cards to be described by the children. All children produced at least one passive and their overall number exceeded passives in prior studies; reversed roles were negligible. In a subsequent image description task, passives were elicited in less favorable conditions. Syntactic priming prevailed across tasks. A procedural account of the production of passives and of the effect of priming is provided, which supports the argument for children’s early competence to compute verbal passives.
The comprehension of Italian negation in Mandarin-Italian sequential bilingual children
Authors: Hu Shenai , Vender Maria , Fiorin Gaetano , Delfitto Denis
Published: November 2018

This study investigates how sequential bilingual Mandarin-speaking children who had more than three years of exposure to Italian comprehended Italian negative sentences in comparison with affirmative ones. Sixteen bilingual children and 16 Italian monolingual peers were tested using a truth-value judgment task. All children showed greater difficulties in the comprehension of True negatives, indicating that the difficulties in the processing of negation, in the relevant experimental conditions, have a general validity across the two groups. This result can be readily interpreted in the light of the “experiential” theories of negation processing, by means of the two-step simulation hypothesis. In addition, it should be emphasized that bilingual children were more accurate in the comprehension of True negatives than monolingual children, a finding that deserves further investigation.
The Emergence of Nominal Expressions in Spanish-English Early Bilinguals
Authors: Ticio Emma
Published: November 2018

This monograph examines the first syntactic unit in child language by presenting a longitudinal multiple-case study that focuses on the inner structure of nominal expressions in bilingual or monolingual child Spanish. This compilation of case studies offers the first insight on some of the properties of nominal expressions in bilingual or monolingual child Spanish and test some of the current theoretical proposals to analyze the main syntactic properties and operations within the nominal phrase. The findings of the study suggest new directions to address some core questions about monolingual and bilingual language acquisition taking as a point of departure the notion of economy, prevalent in the most recent theoretical discussion. Given the combination of empirical and theoretical discussions, this monograph will be appealing to a broad range of researchers in syntax and language acquisition.
Acceleration of bainitic transformation by introducing AlN in medium carbon steel
Authors: Zhao Xiaojie , Yang Zhinan , Zhang Fucheng , Long Xiaoyan , Chen Chen
Published: November 2018

Shortening the austempering time for bainitic transformation is beneficial for the application of high-performance bainitic steel, which has attracted lots of attentions from materials researchers. It is interesting to find that adding nitrogen, ∼210 ppm, in a medium carbon steel can effectively accelerate the bainitic transformation process. Analysis results reveal that the heterogeneous nucleation sites provided by AlN particles should be mainly responsible for the accelerated bainitic transformation.
AKT phosphorylation sites of Ser473 and Thr308 regulate AKT degradation
Authors: Wei Yingze , Zhou Jianyun , Yu Haiyan , Jin Xiaoxia
Published: November 2018

Protein kinase B (AKT) is a serine-threonine kinase that mediates diverse cellular processes in a variety of human diseases. Phosphorylation is always the best studied posttranslational modification of AKT and a connection between phosphorylation and ubiquitination has been explored recently. Ubiquitination of AKT is an important step for its phosphorylation and activation, while whether phosphorylated AKT regulated its ubiquitination status is still unknow. In the present study, we mimic dephosphorylation of AKT by using mutagenesis techniques at both Thr308 and Ser473 into Alanine (AKT-2A). After losing phosphorylation activity, AKT enhances its degradation and prevents itself release from the plasma membrane after insulin stimulation. Fourthermore, AKT-2A is found to be degraded through ubiquitin- proteasome pathway which declared that un-phosphorylation of AKT at both Ser473 and Thr308 sites increases its ubiquitination level. In conclusion, AKT phosphorylated at Ser473 and Thr308 sites have a significant effect on its ubiquitination status.

Abbreviations: AKT: Protein kinase B; Ser: serine; Thr: threonine; IF: immunofluorescence; Epo: Epoxomicin; Baf: Bafilomycin; PBS: phosphate buffer solution
Comparison CCEM-K4.2017 of 10 pF and 100 pF capacitance standards
Authors: Gournay P , Rolland B , Chayramy R , Overney F , Yang Y , Huang L , Lu Z , Wang Y , Koffman A , Johnson L , Xie R , Belliss J , Giblin S , Thornton B , Schurr J , Lee J , Semenov Y
Published: November 2018

In 2017 the Consultative Committee for Electricity and Magnetism (CCEM) commissioned a key comparison of electrical capacitance standards, the second time this quantity has been compared since the implementation of the Mutual Recognition Agreement by the Comité International des Poids et Mesures (CIPM—MRA) in 1999. This comparison—CCEM-K4.2017—was piloted by the Bureau International des Poids et Mesures (BIPM) and included seven National Metrology Institutes (NMI) belonging to four Regional Metrology Organizations.

The measuring scheme adopted for the comparison was that of a star comparison consisting of a set of bilateral comparisons between the participating NMIs and the BIPM, whose capacitance reference base served as a common reference. For each of the bilateral comparisons, the measurands were the capacitance values of 10 pF travelling standard capacitors belonging to the NMIs and, optionally, the values of 100 pF standards.

All the participants have been chosen from those able to realize and maintain a representation of the farad at the best known level of accuracy. Four of them, including the BIPM, were taking their traceability from dc or ac quantum Hall effect standards and, the four others, from a calculable capacitor.

The comparison results analysis have evidenced an agreement within about ±5 parts in 108 for the mandatory 10 pF measurements and within about ±10 parts in 108 for the optional 100 pF measurements. Also, excepted for one of the participants, a good agreement has been found for the ratio 100 pF:10 pF (within ±5 parts in 108).

In addition to the comparison, it has been possible to evaluate the difference between the value of R
K (von Klitzing constant) measured by electrical means from calculable capacitors and its last CODATA recommended value (CODATA 2014 adjustment). A difference of (43 ± 23) parts in 109 (k = 1) has been found which is consistent with the difference that can be computed from the experimental data used in the CODATA 2014 adjustment of fundamental constants.

This report presents the details of the measurements and analysis having led to these results.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
Authors: Asgari Ehsaneddin , Münch Philipp C , Lesker Till R , McHardy Alice C , Mofrad Mohammad R K
Published: November 2018

Identifying distinctive taxa for micro-biome-related diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on the accuracy of micro-biome analysis techniques. We propose an alignment- and reference- free subsequence based 16S rRNA data analysis, as a new paradigm for micro-biome phenotype and biomarker detection. Our method, called DiTaxa, substitutes standard operational taxonomic unit (OTU)-clustering by segmenting 16S rRNA reads into the most frequent variable-length subsequences. We compared the performance of DiTaxa to the state-of-the-art methods in phenotype and biomarker detection, using human-associated 16S rRNA samples for periodontal disease, rheumatoid arthritis and inflammatory bowel diseases, as well as a synthetic benchmark dataset. DiTaxa performed competitively to the k-mer based state-of-the-art approach in phenotype prediction while outperforming the OTU-based state-of-the-art approach in finding biomarkers in both resolution and coverage evaluated over known links from literature and synthetic benchmark datasets.

Availability and implementation

DiTaxa is available under the Apache 2 license at http://llp.berkeley.edu/ditaxa.

Supplementary information

Supplementary data are available at Bioinformatics online.
CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes
Authors: Sun Jiamin , Liu Hao , Liu Jianxiao , Cheng Shikun , Peng Yong , Zhang Qinghua , Yan Jianbing , Liu Hai-Jun , Chen Ling-Ling
Published: November 2018

CRISPR-Local is a high-throughput local tool for designing single-guide RNAs (sgRNAs) in plants and other organisms that factors in genetic variation and is optimized to generate genome-wide sgRNAs. CRISPR-Local outperforms other sgRNA design tools in the following respects: (i) designing sgRNAs suitable for non-reference varieties; (ii) screening for sgRNAs that are capable of simultaneously targeting multiple genes; (iii) saving computational resources by avoiding repeated calculations from multiple submissions and (iv) running offline, with both command-line and graphical user interface modes and the ability to export multiple formats for further batch analysis or visualization. We have applied CRISPR-Local to 71 public plant genomes, using both CRISPR/Cas9 and CRISPR/cpf1 systems.

Availability and implementation

CRISPR-Local can be freely downloaded from http://crispr.hzau.edu.cn/CRISPR-Local/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters
Authors: Casto Amanda M , Adler Amanda L , Makhsous Negar , Crawford Kristen , Qin Xuan , Kuypers Jane M , Huang Meei-Li , Zerr Danielle M , Greninger Alexander L
Published: November 2018

Background

Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone.

Methods

Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study.

Results

We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host.

Conclusions

This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.
SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)
Authors: Formenti Giulio , Chiara Matteo , Poveda Lucy , Francoijs Kees-Jan , Bonisoli-Alquati Andrea , Canova Luca , Gianfranceschi Luca , Horner David Stephen , Saino Nicola
Published: November 2018

Background

The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica).

Findings

As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp.

Conclusions

This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
Forcing and satisfaction in Kripke models of intuitionistic arithmetic
Authors: Abiri Maryam , Moniri Morteza , Zaare Mostafa
Published: November 2018

We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\varphi$ such that satisfaction of $\varphi$ in any classical structure attached to a node of a Kripke model of intuitionistic predicate logic deciding atomic formulas implies its forcing in that node. We also define a class of $\mathsf{E}$-formulas with the property that their forcing coincides with their classical satisfiability in Kripke models which decide atomic formulas. We also prove that any formula with this property is an $\mathsf{E}$-formula. Kripke models of intuitionistic arithmetical theories usually have this property. As a consequence, we prove a new conservativity result for Peano arithmetic over Heyting arithmetic.
Two-Tier Lyme Disease Serology Test Results Can Vary According to the Specific First-Tier Test Used
Authors: Maulden Alexandra B , Garro Aris C , Balamuth Fran , Levas Michael N , Bennett Jonathan E , Neville Desiree N , Branda John A , Nigrovic Lise E
Published: November 2018

Background

Variability in 2-tier Lyme disease test results according to the specific first-tier enzyme immunoassay (EIA) in children has not been examined rigorously. In this study, we compared paired results of clinical 2-tier Lyme disease tests to those of the C6 peptide EIA followed by supplemental immunoblotting (C6 2-tier test).

Methods

We performed a prospective cohort study of children aged ≥1 to ≤21 years who were undergoing evaluation for Lyme disease in the emergency department at 1 of 6 centers located in regions in which Lyme disease is endemic. The clinical first-tier test and a C6 EIA were performed on the same serum sample with supplemental immunoblotting if the first-tier test result was either positive or equivocal. We compared the results of the paired clinical and C6 2-tier Lyme disease test results using the McNemar test.

Results

Of the 1714 children enrolled, we collected a research serum sample from 1584 (92.4%). The clinical 2-tier EIA result was positive in 316 (19.9%) children, and the C6 2-tier test result was positive or equivocal in 295 (18.6%) children. The clinical and C6 2-tier test results disagreed more often than they would have by chance alone (P = .002). Of the 39 children with either a positive clinical or C6 2-tier test result alone, 2 children had an erythema migrans (EM) lesion, and 29 had symptoms compatible with early disseminated Lyme disease.

Conclusions

Two-tier Lyme disease test results differed for a substantial number of children on the basis of the specific first-tier test used. In children for whom there is a high clinical suspicion for Lyme disease and who have an initially negative test result, clinicians should consider retesting for Lyme disease.
Function words in statistical machine-translated Chinese and original Chinese: A study into the translationese of machine translation systems
Authors: Kuo Chen-li
Published: November 2018

Statistical approaches have become the mainstream in machine translation (MT), for their potential in producing less rigid and more natural translations than rule-based approaches. However, on closer examination, the uses of function words between statistical machine-translated Chinese and the original Chinese are different, and such differences may be associated with translationese as discussed in translation studies. This article examines the distribution of Chinese function words in a comparable corpus consisting of MTs and the original Chinese texts extracted from Wikipedia. An attribute selection technique is used to investigate which types of function words are significant in discriminating between statistical machine-translated Chinese and the original texts. The results show that statistical MT overuses the most frequent function words, even when alternatives exist. To improve the quality of the end product, developers of MT should pay close attention to modelling Chinese conjunctions and adverbial function words. The results also suggest that machine-translated Chinese shares some characteristics with human-translated texts, including normalization and being influenced by the source language; however, machine-translated texts do not exhibit other characteristics of translationese such as explicitation.
Archives
Authors: Zeitlyn David
Published: November 2018

Archives and archival studies have an increasingly high profile within anthropology. The term gets used to cover several different fields: in theory it is used to talk about how governments control their populations, including by controlling what sort of history gets written (Derrida 1995 cited under Key Monographs), and generalizing from this, also by controlling how the population thinks about the past and future and about political alternatives (see Foucault 2002 cited under Key Monographs). At a more specific level, one focused more on particulars, archives have become the focus of research in historical anthropology and memory (though the parallel between archives and memory is itself questionable). See the separate Oxford Bibliographies article “Memory.” Studies are now being undertaken of how archives are created and how archivists do their work on the basis of parallels with museum studies. See the separate Oxford Bibliographies article “Museum Anthropology.” Digital archives enable new forms of research, although some and perhaps even most of the conceptual issues around them as archives are in fact the same as for analogue archives, and the digital exponents (who no longer warrant being called pioneers) risk ignoring important precedents and having to relearn the same lessons as their predecessors. The term “archives” can identify the repositories of material (buildings, suites of rooms, or a web address) and the materials contained therein. There is often slippage between these two senses, and some authors pit them against each other. Professional archivists usually discuss “an archives”: the word is plural (because one building/website contains many files). By contrast, theorists who use the idea of records in an extended (metaphorical) sense, following Foucault 2002 and Derrida 1995 (both cited under Key Monographs), discuss the singular “archive,” often with a definite article, so we have “the archive” and sometimes even “the Archive.”
2001: A Space Odyssey
Authors: Abrams Nathan
Published: November 2018

The film 2001: A Space Odyssey (1968) is regarded as one of the greatest science fiction movies ever made. It occupies number one on the American Film Institute’s top ten science fiction films and fifteenth place overall in its top one hundred movies list. Its revolutionary storyline and techniques mean that it continues to inspire filmmakers today. Lines and scenes from the movie have become legendary and are regularly quoted in film, television, and popular culture. But while all of Kubrick’s films were complex and multilayered, compounded by his customary refusal to explain his intentions, 2001 is perhaps the most complex, multilayered, and enigmatic of all. As with all his films, it requires multiple viewings to unlock its secrets. This complexity has led to an ever-expanding scholarly literature on 2001 all detailing new interpretations. Books and articles range from production and reception histories to intricate analyses. Additional resources are available in the separate Oxford Bibliographies article in Cinema and Media Studies “Stanley Kubrick”; please cross-check. They have not been repeated here.
Tenofovir Alafenamide in Multimorbid HIV-Infected Patients With Prior Tenofovir-Associated Renal Toxicity
Authors: Walti Laura N , Steinrücken Julia , Rauch Andri , Wandeler Gilles
Published: November 2018

Although the use of tenofovir alafenamide (TAF), a new prodrug of tenofovir, was safe and efficacious in clinical trials, real-world data from multimorbid individuals are scarce. Among 10 persons living with HIV with previous tenofovir disoproxil fumarate–induced nephrotoxicity, renal function remained stable, and proteinuria decreased in several patients after the switch to TAF.
Running in the Family? Structural Brain Abnormalities and IQ in Offspring, Siblings, Parents, and Co-twins of Patients with Schizophrenia
Authors: de Zwarte Sonja M C , Brouwer Rachel M , Tsouli Andromachi , Cahn Wiepke , Hillegers Manon H J , Hulshoff Pol Hilleke E , Kahn René S , van Haren Neeltje E M
Published: November 2018

Structural brain abnormalities and cognitive deficits have been reported in patients with schizophrenia and to a lesser extent in their first-degree relatives (FDRs). Here we investigated whether brain abnormalities in nonpsychotic relatives differ per type of FDR and how these abnormalities are related to intelligent quotient (IQ). Nine hundred eighty individuals from 5 schizophrenia family cohorts (330 FDRs, 432 controls, 218 patients) were included. Effect sizes were calculated to compare brain measures of FDRs and patients with controls, and between each type of FDR. Analyses were repeated with a correction for IQ, having a nonpsychotic diagnosis, and intracranial volume (ICV). FDRs had significantly smaller ICV, surface area, total brain, cortical gray matter, cerebral white matter, cerebellar gray and white matter, thalamus, putamen, amygdala, and accumbens volumes as compared with controls (ds < −0.19, q < 0.05 corrected). Offspring showed the largest effect sizes relative to the other FDRs; however, none of the effects in the different relative types survived correction for multiple comparisons. After IQ correction, all effects disappeared in the FDRs after correction for multiple comparisons. The findings in FDRs were not explained by having a nonpsychotic disorder and were only partly explained by ICV. FDRs show brain abnormalities that are strongly covarying with IQ. On the basis of consistent evidence of genetic overlap between schizophrenia, IQ, and brain measures, we suggest that the brain abnormalities in FDRs are at least partly explained by genes predisposing to both schizophrenia risk and IQ.
Examining the external validity of the CRUZA study, a randomized trial to promote implementation of evidence-based cancer control programs by faith-based organizations
Authors: Allen Jennifer Dacey , Shelton Rachel C , Kephart Lindsay , Tom Laura S , Leyva Bryan , Ospino Hosffman , Cuevas Adolfo G
Published: November 2018

The CRUZA trial tested the efficacy of an organizational-level intervention to increase capacity among Catholic parishes to implement evidence-based interventions (EBIs) for cancer control. This paper examines the external generalizability of the CRUZA study findings by comparing characteristics of parishes that agreed to participate in the intervention trial versus those that declined participation. Sixty-five Roman Catholic parishes that offered Spanish-language mass in Massachusetts were invited to complete a four-part survey assessing organization-level characteristics that, based on the Consolidated Framework for Implementation Research (CFIR), may be associated with EBI implementation. Forty-nine parishes (75%) completed the survey and were invited to participate in the CRUZA trial, which randomized parishes to either a “capacity enhancement intervention” or a “standard dissemination” group. Of these 49 parishes, 31 (63%) agreed to participate in the trial, whereas 18 parishes (37%) declined participation. Parishes that participated in the CRUZA intervention trial were similar to those that did not participate with respect to “inner organizational setting” characteristics of the CFIR, including innovation and values fit, implementation climate, and organizational culture. Change commitment, a submeasure of organizational readiness that reflects the shared resolve of organizational members to implement an innovation, was significantly higher among the participating parishes (mean = 3.93, SD = 1.08) as compared to nonparticipating parishes (mean = 3.27, SD = 1.08) (Z = −2.16, p = .03). Parishes that agreed to participate in the CRUZA intervention trial were similar to those that declined participation with regard to organizational characteristics that may predict implementation of EBIs. Pragmatic tools to assess external generalizability in community-based implementation trials and to promote readiness among faith-based organizations to implement EBIs are needed to enhance the reach and impact of public health research.

Clinical Trial information: The CRUZA trial identifier number with clinicaltrials.gov is NCT01740219.
Transient Receptor Potential Ion Channels Mediate Adherens Junctions Dysfunction in a Toluene Diisocyanate-Induced Murine Asthma Model
Authors: Yao Lihong , Chen Shuyu , Tang Haixiong , Huang Peikai , Wei Shushan , Liang Zhenyu , Chen Xin , Wang Hongyu , Tao Ailin , Chen Rongchang , Zhang Qingling
Published: November 2018

Disruption of epithelial cell-cell junctions is essential for the initiation and perpetuation of airway inflammation in asthma. We’ve previously reported compromised epithelial barrier integrity in a toluene diisocyanate (TDI)-induced occupational asthma model. This study is aimed to explore the role of transient receptor potential vanilloid 4 (TRPV4) and transient receptor potential ankyrin 1 (TRPA1) in the dysfunction of adherens junctions in TDI-induced asthma. Mice were sensitized and challenged with TDI for a chemical-induced asthma model. Selective blockers of TRPV4 glycogen synthase kinase (GSK)2193874, 5 and 10 mg/kg) and TRPA1 (HC030031, 10 and 20 mg/kg) were intraperitoneally given to the mice. Immunohistochemistry revealed different expression pattern of TRPV4 and TRPA1 in lung. TDI exposure increased TRPV4 expression in the airway, which can be suppressed by GSK2193874, while treatment with neither TDI alone nor TDI together with HC030031 led to changes of TRPA1 expression in the lung. Blocking either TRPV4 or TRPA1 blunted TDI-induced airway hyperreactivity, airway neutrophilia and eosinophilia, as well as Th2 responses in a dose-dependent manner. At the same time, membrane levels of E-cadherin and β-catenin were significantly decreased after TDI inhalation, which were inhibited by GSK2193874 or HC030031. Moreover, GSK2193874 and HC030031 also suppressed serine phosphorylation of glycogen synthase kinase 3β, tyrosine phosphorylation of β-catenin, as well as activation and nuclear transport of β-catenin in mice sensitized and challenged with TDI. Our study suggested that both TRPV4 and TRPA1 contribute critically to E-cadherin and β-catenin dysfunction in TDI-induced asthma, proposing novel therapeutic targets for asthma.
Histopathological and Molecular Signatures of a Mouse Model of Acute-on-Chronic Alcoholic Liver Injury Demonstrate Concordance With Human Alcoholic Hepatitis
Authors: Furuya Shinji , Cichocki Joseph A , Konganti Kranti , Dreval Kostiantyn , Uehara Takeki , Katou Yuuki , Fukushima Hisataka , Kono Hiroshi , Pogribny Igor P , Argemi Josepmaria , Bataller Ramon , Rusyn Ivan
Published: November 2018

Human alcoholic hepatitis (AH) carries a high mortality rate. AH is an acute-on-chronic form of liver injury characterized by hepatic steatosis, ballooned hepatocytes, neutrophil infiltration, and pericellular fibrosis. We aimed to study the pathogenesis of AH in an animal model which combines chronic hepatic fibrosis with intragastric alcohol administration. Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (up to 25 g/kg/day for 3 weeks) was administered continuously to mice via a gastric feeding tube, with or without one-half dose of CCl4. Liver and serum markers and liver transcriptome were evaluated to characterize acute-on-chronic-alcoholic liver disease in our model. CCl4 or alcohol treatment alone induced liver fibrosis or steatohepatitis, respectively, findings that were consistent with expected pathology. Combined treatment resulted in a marked exacerbation of liver injury, as evident by the development of inflammation, steatosis, and pericellular fibrosis, pathological features of human AH. E. coli and Candida were also detected in livers of mice cotreated with CCl4 and alcohol, indicating pathogen translocation from gut to liver, similar to human AH. Importantly, liver transcriptomic changes specific to combined treatment group demonstrated close concordance with pathways perturbed in patients with severe AH. Overall, mice treated with CCl4 and alcohol displayed key molecular and pathological characteristics of human AH—pericellular fibrosis, increased hepatic bacterial load, and dysregulation of the same molecular pathways. This model may be useful for developing therapeutics for AH.
Genomewide Transcriptome Profiles Reveal How Bacillus subtilis Lipopeptides Inhibit Microsclerotia Formation in Verticillium dahliae
Authors: Yu Dimei , Fang Yulin , Tang Chen , Klosterman Steven J. , Tian Chengming , Wang Yonglin
Published: November 2018

Verticillium dahliae is a soilborne fungus and the primary causal agent of vascular wilt diseases worldwide. The fungus produces melanized microsclerotia that are crucially important for the survival and spread of V. dahliae. There are no fungicides available that are both effective and environmentally friendly to suppress the fungus. Previously, Bacillus subtilis C232 was isolated from soil and was demonstrated to suppress microsclerotia formation in V. dahliae. In this study, liquid chromatography coupled with mass spectrometry revealed that the antifungal substance is actually a mixture of lipopeptides. Exposure of V. dahliae to these lipopeptides resulted in hyphal swelling, cell lysis, and downregulation of melanin-related genes. RNA sequencing analyses of the lipopeptide-suppressed transcriptome during microsclerotial development revealed that 5,974 genes (2,131 upregulated and 3,843 downregulated) were differentially expressed versus nonsuppressive conditions. Furthermore, gene ontology enrichment analyses revealed that genes involved in response to stress, cellular metabolic processes, and translation were significantly enriched. Additionally, the lipopeptides inhibited expression of genes associated with secondary metabolism, protein catabolism, and the high-osmolarity glycerol response signaling pathway. Together, these findings provide evidence for the mechanism by which B. subtilis lipopeptides suppress microsclerotia formation. The transcriptomic insight garnered here may facilitate the development of biological agents to combat Verticillium wilt.
Should we be targeting sleep architecture to more effectively treat schizophrenia?
Authors: Luu Brent , Rodway George W. , Rice Elizabeth
Published: November 2018

The sleep architecture (or sleep kinetics) of schizophrenia is different from that of other mental illnesses, including major depressive disorder. However, clinicians rarely consider these parameters in clinical settings during treatment. This article discusses the use of polysomnography to characterize the sleeping patterns of patients diagnosed with schizophrenia and the positive influence of clozapine on sleep in patients with schizophrenia.
Postapplication Advisement for U.S. Medical School Reapplicants: One School’s Program
Authors: Ballejos Marlene P. , Schmitt Cheryl L. , McKinney Kara L. , Sapien Robert
Published: November 2018

Problem

Reapplicants make up over one-quarter of U.S. medical school applicants. Postapplication advisement (PAA) can provide potential reapplicants with concrete strategies for improvement, a contextualized basis for their scores, and a realistic idea of their chances for success. However, more data showing the effectiveness of PAA and an analysis of best practices are needed for PAA programs to be more widely adopted.

Approach

In 2010, the University of New Mexico School of Medicine (UNM SOM) created a PAA program that involves a postapplication seminar (PAS), mandatory self-assessment and action plan development, and an individual consult with an admissions dean to prepare participants for reapplication.

Outcomes

From 2010 to 2016, 892 applicants who interviewed and were rejected at UNM SOM were eligible to participate in PAA. Of these, 478 (53.6%) chose to participate in PAA over the seven-year period. Males had a higher participation rate (246/430; 57.2%) compared with females (232/461; 50.3%; P = .04). African Americans had a higher participation rate (12/17; 70.6%) and American Indian/Alaska Natives had a lower participation rate (17/64; 26.6%) than any other race/ethnicity. Of reapplicants who were subsequently accepted, 140/178 (78.7%) attended PAS and a consult, and 7/178 (3.9%) attended PAS only, compared with 31/178 (17.4%) of subsequently accepted reapplicants who did not participate in any PAA (P < .001).

Next Steps

Additional research should focus on the best approach for assisting reapplicants with prioritizing areas for improvement in their application. Demographic data may be used to target outreach to specific populations.
Comparison of Perioperative Systemic Lidocaine or Systemic Ketamine in Acute Pain Management of Patients With Opioid Use Disorder After Orthopedic Surgery
Authors: Sahmeddini Mohammad Ali , Khosravi Mohammad Bagher , Farbood Arash
Published: November 2018

Introduction and Aims:

Patients with opioid use disorder experience great challenges during acute pain management due to opioid tolerance or withdrawal symptoms. Previous studies have recommended the use of adjuvant drugs in these patients. In this study, we compared the effect of intraoperative lidocaine with ketamine in postoperative pain management of these patients.

Design and Methods:

In this randomized clinical trial, 180 patients with opioid use disorder who underwent orthopedic surgery under general anesthesia were randomly allocated into 3 groups. Patients in groups A, B, and C received intravenous lidocaine, ketamine, or normal saline, respectively, during the operation. Then, postoperative pain scores, analgesic requirements, patient satisfaction, and patient sleepiness were recorded and compared among the 3 groups.

Results:

Numerical rating scales during the first hour postoperation were significantly lower in the lidocaine group than in the ketamine or control group (P < 0.001). The mean total amount of morphine consumption during the first 24-hour postoperation was 14.49 ± 26.89, 16.59 ± 30.65, and 21.72 ± 43.29 mg in the lidocaine, ketamine, and control group, respectively, being significantly lower in the lidocaine group in comparison with the other groups (P < 0.001). Patients in the lidocaine group were less restless, calmer, and less drowsy than patients in the ketamine and control group (P < 0.001).

Discussion and Conclusion:

According to these findings, systemic lidocaine is more effective than systemic ketamine to improve the quality of acute pain management without causing any significant complications in patients with opioid use disorder.