bluuebunny/crossref_metadata_2025 huggingface dataset:
Using history to foster critical scientific thinking: Aristotle and Galileo's debate resolved through high-speed motion tracking in the classroom
Authors: Stadlbauer Josef M. , Kehrer Lukas , Bauer Siegfried
Published: November 2018

In his Discorsi, Galileo aimed to correct centuries of Aristotelian “unreason” concerning the physics of falling objects by introducing a thought experiment that pointed out contradictions when combinations of one light and one heavy body are dropped. Inspired by Galileo's story, we sought to formulate research questions and design experiments for students to enable independent learning based on the history of science. The experiments involve commonly used or inexpensive equipment and free software, and show that Aristotle and Galileo did not disagree about falling objects, but were focusing on different kinds of motion. We assess data generated by high-speed video motion tracking of the fall of various combinations of simple handmade paper cones, following closely the discussion between Simplicio, Salviati and Sagredo in the Discorsi, and demonstrate that every statement in Galileo's reductio ad absurdum holds true and that his argument is in fact free of contradiction.
Effects of intelligibility on within- and cross-modal sentence recognition memory for native and non-native listeners
Authors: Keerstock Sandie , Smiljanić Rajka
Published: November 2018

The goal of the study was to examine whether enhancing the clarity of the speech signal through conversational-to-clear speech modifications improves sentence recognition memory for native and non-native listeners, and if so, whether this effect would hold when the stimuli in the test phase are presented in orthographic instead of auditory form (cross-modal presentation). Sixty listeners (30 native and 30 non-native English) participated in a within-modal (i.e., audio-audio) sentence recognition memory task (Experiment I). Sixty different individuals (30 native and 30 non-native English) participated in a cross-modal (i.e., audio-textual) sentence recognition memory task (Experiment II). The results showed that listener-oriented clear speech enhanced sentence recognition memory for both listener groups regardless of whether the acoustic signal was present during the test phase (Experiment I) or absent (Experiment II). Compared to native listeners, non-native listeners had longer reaction times in the within-modal task and were overall less accurate in the cross-modal task. The results showed that more cognitive resources remained available for storing information in memory during processing of easier-to-understand clearly produced sentences. Furthermore, non-native listeners benefited from signal clarity in sentence recognition memory despite processing speech signals in a cognitively more demanding second language.
Evaluation of Carbapenems for Treatment of Multi- and Extensively Drug-Resistant
Mycobacterium tuberculosis
Authors: van Rijn Sander P. , Zuur Marlanka A. , Anthony Richard , Wilffert Bob , van Altena Richard , Akkerman Onno W. , de Lange Wiel C. M. , van der Werf Tjip S. , Kosterink Jos G. W. , Alffenaar Jan-Willem C.
Published: November 2018

Multi- and extensively drug-resistant tuberculosis (M/XDR-TB) has become an increasing threat not only in countries where the TB burden is high but also in affluent regions, due to increased international travel and globalization. Carbapenems are earmarked as potentially active drugs for the treatment of
Mycobacterium tuberculosis
.
PPE37 Is Essential for
Mycobacterium tuberculosis
Heme-Iron Acquisition (HIA), and a Defective PPE37 in
Mycobacterium bovis
BCG Prevents HIA
Authors: Tullius Michael V. , Nava Susana , Horwitz Marcus A.
Published: November 2018

Mycobacterium tuberculosis
, one of the world’s leading causes of death, must acquire nutrients, such as iron, from the host to multiply and cause disease. Iron is an essential metal and
M. tuberculosis
possesses two different systems to acquire iron from its environment: siderophore-mediated iron acquisition (SMIA) and heme-iron acquisition (HIA), involving uptake and degradation of heme to release ferrous iron.
Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential
Authors: Bulow Christopher , Langdon Amy , Hink Tiffany , Wallace Meghan , Reske Kimberly A. , Patel Sanket , Sun Xiaoqing , Seiler Sondra , Jones Susan , Kwon Jennie H. , Burnham Carey-Ann D. , Dantas Gautam , Dubberke Erik R.
Published: November 2018

The spread of multidrug resistance among pathogenic organisms threatens the efficacy of antimicrobial treatment options. The human gut serves as a reservoir for many drug-resistant organisms and their resistance genes, and perturbation of the gut microbiome by antimicrobial exposure can open metabolic niches to resistant pathogens. Once established in the gut, antimicrobial-resistant bacteria can persist even after antimicrobial exposure ceases. Strategies to prevent multidrug-resistant organism (MDRO) infections are scarce, but autologous fecal microbiota transplantation (autoFMT) may limit gastrointestinal MDRO expansion. AutoFMT involves banking one’s feces during a healthy state for later use in restoring gut microbiota following perturbation. This pilot study evaluated the effect of amoxicillin-clavulanic acid (Amox-Clav) exposure and autoFMT on gastrointestinal microbiome taxonomic composition, resistance gene content, and metabolic capacity. Importantly, we found that metabolic capacity was perturbed even in cases where gross phylogeny remained unchanged and that autoFMT was safe and well tolerated.
DNA metabarcoding from sample fixative as a quick and voucher-preserving biodiversity assessment method
Authors: Zizka Vera M.A. , Leese Florian , Peinert Bianca , Geiger Matthias F.
Published: November 2018

Metabarcoding is a powerful, increasingly popular tool for biodiversity assessment, but it still suffers from some drawbacks (specimen destruction, separation, and size sorting). In the present study, we tested a non-destructive protocol that excludes any sample sorting, where the ethanol used for sample preserving is filtered and DNA is extracted from the filter for subsequent DNA metabarcoding. When tested on macroinvertebrate mock communities, the method was widely successful but was unable to reliably detect mollusc taxa. Three different protocols (no treatment, shaking, and freezing) were successfully applied to increase DNA release to the fixative. The protocols resulted in similar success in taxa detection (6.8–7 taxa) but differences in read numbers assigned to taxa of interest (33.8%–93.7%). In comparison to conventional bulk sample metabarcoding of environmental samples, taxa with pronounced exoskeleton and small-bodied taxa were especially underrepresented in ethanol samples. For EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa, which are important for determining stream ecological status, the methods detected 46 OTUs in common, with only 4 unique to the ethanol samples and 10 to the bulk samples. These results indicate that fixative-based metabarcoding is a non-destructive, time-saving alternative for biodiversity assessments focussing on taxa used for ecological status determination. However, for a comprehensive assessment on total invertebrate biodiversity, the method may not be sufficient, and conventional bulk sample metabarcoding should be applied.
Non-minimal matter-geometry coupling in the Bianchi-V spacetime within the formalism of f(R, T) = f1(R) + f2(R)f3(T) cosmology
Authors: Bhardwaj Vinod Kumar
Published: November 2018

The models of [Formula: see text] gravity are efficient in describing a non-minimal coupling between geometry and matter. In this paper, the extended theory of gravity describes the non-minimal coupling between matter and geometry using special cosmological model of [Formula: see text] in Bianchi-V spacetime; whose functional relations are [Formula: see text] and [Formula: see text], where [Formula: see text] is a constant. The Einstein’s field equation has been solved by taking special choice of scale factor as [Formula: see text], where [Formula: see text], [Formula: see text] and [Formula: see text] are constants. The energy and other stability conditions obtained in this paper explain the physical behavior of phase transition of universe and it also confirms the stability of the derived model.
Simulating the induced gravitational collapse scenario of long gamma-ray bursts
Authors: Rueda J. A. , Ruffini R. , Becerra L. M. , Fryer C. L.
Published: November 2018

We present the state-of-the-art of the numerical simulations of the supernova (SN) explosion of a carbon-oxygen core [Formula: see text] that forms a compact binary with a neutron star (NS) companion, following the induced gravitational collapse (IGC) scenario of long gamma-ray bursts (GRBs) associated with type Ic supernovae (SNe). We focus on the consequences of the hypercritical accretion of the SN ejecta onto the NS companion which either becomes a more massive NS or gravitationally collapses forming a black hole (BH). We summarize the series of results on this topic starting from the first analytic estimates in 2012 all the way up to the most recent three-dimensional (3D) smoothed-particle-hydrodynamics (SPH) numerical simulations in 2018. We present a new SN ejecta morphology, highly asymmetric, acquired by binary interaction and leading to well-defined, observable signatures in the gamma- and X-rays emission of long GRBs.
Timing of strain partitioning and magmatism in the Scottish Scandian collision, evidence from the high Ba–Sr Orkney granite complex
Authors: Lundmark Anders Mattias , Augland Lars Eivind , Bjerga Audun Dalene
Published: November 2018

The Orkney granite complex dominates the outcropping basement on Orkney, Scotland. It comprises a grey and a pink variably foliated granite, and structurally younger pegmatites and aplites. Based on geochemical characteristics the granites are assigned to the Scottish high Ba–Sr granites. The granites are deformed by synmagmatic extensional east–west-trending mylonite zones. These are locally overprinted by similarly oriented extensional phyllonites and, in one case, by similarly oriented extensional faults. The grey and the pink granites are dated by zircon U–Pb CA-ID-TIMS to 431.93 ± 0.46 and 430.26 ± 0.92 Ma, respectively. An aplite cutting mylonitic granite and cut by phyllonite is dated to 428.50 ± 0.31 Ma. We interpret the shear zones to record north–south extension during emplacement and cooling of the granites, likely at a shallow crustal depth (4–12 km). The extension is best explained by a subsidiary pull-apart structure related to displacement on the Great Glen Fault. In this case, the Orkney granite complex dates transcurrent faulting to 432–429 Ma, coeval with the 431–429 Ma Moine Thrust. This indicates that strain partitioning and high Ba–Sr magmatism across the Scottish Highlands was an immediate response to attempted subduction of Avalonia beneath Laurentia during the Scandian collision.

Supplementary material:
Geochronological and geochemical data (Tables 1 and 2) as spreadsheets are available at
https://doi.org/10.6084/m9.figshare.c.4304387
“How Else Should It Work?” A Grounded Theory of Pre-College Students’ Understanding of Computing Devices
Authors: Rücker Michael T. , Pinkwart Niels
Published: November 2018

In order to understand and evaluate computing technology in their environment, students first need to be able to identify it. This task becomes increasingly difficult, however, as computing systems become more and more ubiquitous and invisible. Based on the analysis of semi-structured focus interviews with 28 German pre-college students, we present a grounded theory of their conceptions and reasoning related to the identification of computing within technical devices. At its core is the finding that many students seemed to differentiate technical artifacts with respect to three conceived levels of capability. Many household appliances, for instance, were very well seen as electronic and programmed, but still as too limited in their capability to warrant the presence of a “real” computer or to be related to informatics. Given the increasing versatility, power, and associated risks of modern embedded systems as well as the advent of the internet of things, this issue should clearly be addressed. Based on our grounded theory, we propose some first ideas for how this might be done.
Automated Equivalence Checking of Concurrent Quantum Systems
Authors: Ardeshir-Larijani Ebrahim , Gay Simon J. , Nagarajan Rajagopal
Published: November 2018

The novel field of quantum computation and quantum information has gathered significant momentum in the last few years. It has the potential to radically impact the future of information technology and influence the development of modern society. The construction of practical, general purpose quantum computers has been challenging, but quantum cryptographic and communication devices have been available in the commercial marketplace for several years. Quantum networks have been built in various cities around the world and a dedicated satellite has been launched by China to provide secure quantum communication. Such new technologies demand rigorous analysis and verification before they can be trusted in safety- and security-critical applications. Experience with classical hardware and software systems has shown the difficulty of achieving robust and reliable implementations.

We present

CCS
q

, a concurrent language for describing quantum systems, and develop verification techniques for checking equivalence between

CCS
q

processes.

CCS
q

has well-defined operational and superoperator semantics for protocols that are
functional
, in the sense of computing a deterministic input-output relation for all interleavings arising from concurrency in the system. We have implemented QEC (Quantum Equivalence Checker), a tool that takes the specification and implementation of quantum protocols, described in

CCS
q

, and automatically checks their equivalence. QEC is the first fully automatic equivalence checking tool for concurrent quantum systems. For efficiency purposes, we restrict ourselves to Clifford operators in the stabilizer formalism, but we are able to verify protocols over all input states. We have specified and verified a collection of interesting and practical quantum protocols, ranging from quantum communication and quantum cryptography to quantum error correction.
A Survey of Cloudlet-Based Mobile Augmentation Approaches for Resource Optimization
Authors: Nayyer M. Ziad , Raza Imran , Hussain Syed Asad
Published: November 2018

Mobile devices (MDs) face resource scarcity challenges owing to limited energy and computational resources. Mobile cloud computing (MCC) offers a resource-rich environment to MDs for offloading compute-intensive tasks encountering resource scarcity challenges. However, users are unable to exploit its full potential owing to challenges of distance, limited bandwidth, and seamless connectivity between the remote cloud (RC) and MDs in the conventional MCC model. The cloudlet-based solution is widely used to address these challenges. The response of the cloudlet-based solution is faster than the conventional mobile cloud-computing model, rendering it suitable for the Internet of Things (IoT) and Smart Cities (SC). However, with the increase in devices and workloads, the cloudlet-based solution has to deal with resource-scarcity challenges, thus, forwarding the requests to remote clouds. This study has been carried out to provide an insight into existing cloudlet-based mobile augmentation (CtMA) approaches and highlights the underlying limitations for resource optimization. Furthermore, numerous performance parameters have been identified and their detailed comparative analysis has been used to quantify the efficiency of CtMA approaches.
“UTTAM”
Authors: Jain Amita , Jain Minni , Jain Goonjan , Tayal Devendra K.
Published: November 2018

In this article, we propose a system called “UTTAM,” for correcting spelling errors in Hindi language text using supervised learning. Unlike other languages, Hindi contains a large set of characters, words with inflections and complex characters, phonetically similar sets of characters, and so on. The complexity increases the possibility of confusion and occasionally leads to entering a wrong character in a word. The existence of spelling errors in text significantly decreases the accuracy of the available resources, like search engine, text editor, and so on. The proposed work is the first approach to correct non-word (Out of Vocabulary) errors as well as real-word errors simultaneously in a sentence of Hindi language. The proposed method investigates the human behavior, i.e., the type and frequency of spelling errors done by humans in Hindi text. Based on the type and frequency of spelling errors, the heterogeneous data is collected in matrices. This data in matrices is used to generate the suitable candidate words for an input word. After generating candidate words, the Viterbi algorithm is applied to perform the word correction. The Viterbi algorithm finds the best sequence of candidate words to correct the input sentence. For Hindi, this work is the first attempt for real-word error correction. For non-word errors, the experiments show that “UTTAM” performs better than the existing systems SpellGuru and Saksham.
A Design-Time/Run-Time Application Mapping Methodology for Predictable Execution Time in MPSoCs
Authors: Weichslgartner Andreas , Wildermann Stefan , Gangadharan Deepak , Glaß Michael , Teich Jürgen
Published: November 2018

Executing multiple applications on a single MPSoC brings the major challenge of satisfying multiple quality requirements regarding real-time, energy, and so on. Hybrid application mapping denotes the combination of design-time analysis with run-time application mapping. In this article, we present such a methodology, which comprises a design space exploration coupled with a formal performance analysis. This results in several resource reservation configurations, optimized for multiple objectives, with verified real-time guarantees for each individual application. The Pareto-optimal configurations are handed over to run-time management, which searches for a suitable mapping according to this information. To provide any real-time guarantees, the performance analysis needs to be composable and the influence of the applications on each other has to be bounded. We achieve this either by spatial or a novel temporal isolation for tasks and by exploiting composable networks-on-chip (NoCs). With the proposed temporal isolation, tasks of different applications can be mapped to the same resource, while, with spatial isolation, one computing resource can be exclusively used by only one application. The experiments reveal that the success rate in finding feasible application mappings can be increased by the proposed temporal isolation by up to 30% and energy consumption can be reduced compared to spatial isolation.
Histone Demethylase KDM4B Promotes DNA Damage by Activating Long Interspersed Nuclear Element-1
Authors: Xiang Ying , Yan Kai , Zheng Qian , Ke Haiqiang , Cheng Jie , Xiong Wenjun , Shi Xin , Wei Lei , Zhao Min , Yang Fei , Wang Ping , Lu Xing , Fu Li , Lu Xuemei , Li Feng
Published: November 2018

The histone demethylase KDM4B is frequently overexpressed in various cancer types, and previous studies have indicated that the primary oncogenic function of KDM4B is its ability to demethylate H3K9me3 in different tumors, resulting in altered gene expression and genome instability. A genome-wide analysis to evaluate the effect of KDM4B on the global or local H3K9me3 level has not been performed. In this study, we assess whole-genome H3K9me3 distribution in cancer cells and find that H3K9me3 is largely enriched in long interspersed nuclear element-1 (LINE-1). A significant proportion of KDM4B-dependent H3K9me3 was located in evolutionarily young LINE-1 elements, which likely retain retrotransposition activity. Ectopic expression of KDM4B promoted LINE-1 expression, while depletion of KDM4B reduced it. Furthermore, KDM4B overexpression enhanced LINE-1 retrotransposition efficacy, copy number, and associated DNA damage, presumably via the histone demethylase activity of KDM4B. Breast cancer cell lines expressing high levels of KDM4B also exhibited increased LINE-1 expression and copy number compared with other cell lines. Pharmacologic inhibition of KDM4B significantly reduced LINE-1 expression and DNA damage in breast cancer cells with excessive KDM4B. Our study not only identifies KDM4B as a novel regulator of LINE-1, but it also suggests an unexpected oncogenic role for KDM4B overexpression in tumorigenesis, providing clues for the development of new cancer prevention strategies and therapies.

Significance:

The histone demethylase KDM4B promotes tumorigenesis by inducing retrotransposition and DNA damage.
Receipt of Colonoscopy Following Diagnosis of Advanced Adenomas: An Analysis within Integrated Healthcare Delivery Systems
Authors: Chubak Jessica , McLerran Dale , Zheng Yingye , Singal Amit G. , Corley Douglas A. , Doria-Rose V. Paul , Doubeni Chyke A. , Kamineni Aruna , Haas Jennifer S. , Halm Ethan A. , Skinner Celette Sugg , Zauber Ann G. , Wernli Karen J. , Beaber Elisabeth F.
Published: November 2018

Background:

To reduce colorectal cancer incidence and mortality, experts recommend surveillance colonoscopy 3 years after advanced adenoma removal. Little is known about adherence to that interval.

Methods:

We describe patterns of and factors associated with subsequent colonoscopy among persons with ≥3 adenomas and/or ≥1 adenoma with villous/tubulovillous histology in four U.S. integrated healthcare delivery systems. We report Kaplan–Meier estimators of the cumulative percentage of patients undergoing colonoscopy 6 months to 3.5 years after an index colonoscopy with high-risk findings. Combining data from three healthcare systems, we used multivariable logistic regression with inverse probability of censoring weights to estimate ORs and 95% confidence intervals (CI) for associations between patient characteristics and receipt of subsequent colonoscopy.

Results:

Among 6,909 persons with advanced adenomas, the percent receiving a subsequent colonoscopy 6 months to 3.5 years later ranged from 18.3% (95% CI: 11.7%–27.8%) to 59.5% (95% CI: 53.8%–65.2%) across healthcare systems. Differences remained significant in the multivariable model. Patients with ≥3 adenomas were more likely than those with 1 to 2 villous/tubulovillous adenomas to undergo subsequent colonoscopy. Subsequent colonoscopy was also more common for patients ages 60–74 and less common for patients ages 80 to 89 compared with those ages 50 to 54 years at their index colonoscopy. Sex, race/ethnicity, and comorbidity index score were generally not associated with subsequent colonoscopy receipt.

Conclusions:

Colonoscopy within the recommended interval following advanced adenoma was underutilized and varied by healthcare system, age, and number of adenomas.

Impact:

Strategies to improve adherence to surveillance colonoscopy following advanced adenomas are needed.
Bronchial Asthma and Bronchial Hyperresponsiveness and Their Characteristics in Patients with Common Variable Immunodeficiency
Authors: Milota Tomas , Bloomfield Marketa , Parackova Zuzana , Sediva Anna , Bartunkova Jirina , Horvath Rudolf
Published: November 2018

Background: Common variable immunodeficiency (CVID) is one of the most frequent primary immunodeficiencies and is characterized by disturbed immunoglobulin production and dysregulation of the immune system. Results of previous studies suggest a higher prevalence of bronchial asthma (BA) in CVID patients than in the general population. We initiated this study to evaluate lung functions and identify risk factors for BA and bronchial hyperresponsiveness (BHR) in patients with CVID. Methods: Twenty-three patients with CVID were included in this study. In all of them, spirometry and a metacholine bronchoprovocation test were performed. We also investigated the role of atopy, eosinophilic inflammation, and potential risk factors such as gender, age, or immunoglobulin levels at the time of diagnosis. Results: BHR was confirmed in 12 patients (52%), all of whom had normal FEV1 and FEV1/FVC. However, BHR-positive patients had significantly decreased MEF25. BHR-positive patients had also more symptoms related to bronchial obstruction, with 8 of them (35%) being suspected of having BA at the end of the study. A higher prevalence of BHR was found in females, with a relative risk of 2.89. Conclusions: An increased prevalence of BHR and BA was detected in CVID patients compared to the general population. BA may develop despite the disturbed immunoglobulin production, and the majority of patients display nonatopic and noneosinophilic properties. These results suggest a limited role of atopy and eosinophilic inflammation in the pathogenesis of BA in CVID patients.
ВИВЧЕННЯ ПРОТИЗАПАЛЬНОЇ АКТИВНОСТІ СУХОГО ЕКСТРАКТУ З ЛИСТЯ САЛАТУ ПОСІВНОГО
Authors: Puda V. P. , Fira L. S. , Lykhatskyi P. H.
Published: November 2018

Вступ. Проблема фармакологічної корекції запалення, як і раніше, залишається актуальною, оскільки сучасна медицина повністю її не вирішила. Одним із перспективних напрямів створення безпечних та ефективних протизапальних препаратів є фітотерапія. В останні роки підвищився інтерес до препаратів рослинного походження.

Мета дослідження – вивчити протизапальну активність сухого екстракту з листя салату посівного в експерименті з модельованим карагеніновим набряком лапи щурів.

Методи дослідження. При визначенні протизапальної активності екстракту з листя салату посівного використовували безпородних білих щурів-самців масою 180–200 г. Індукцію гострого асептичного запалення проводили шляхом субплантарної ін’єкції 0,1 мл 1 % розчину карагеніну. Досліджуваний зразок екстракту в дозі 100 мг/кг маси тіла вводили піддослідним щурам внутрішньошлунково у профілактичному режимі одноразово за 1 год до індукції запалення. Через 1, 3, 6 та 24 год вимірювали об’єм здорової та ураженої кінцівок за допомогою механічного онкометра. Антиексудативну активність екстракту визначали за ступенем зменшення набряку в піддослідних тварин порівняно з контрольними та виражали у відсотках. Як препарат порівняння використовували диклофенак натрію в дозі 8 мг/кг.

Результати й обговорення. Встановлено, що у групі тварин, які отримували екстракт з листя салату посівного, максимальний позитивний вплив на розвиток набряку спостерігали через 3 год від початку запалення (31,22 %), і тривав він до кінця експерименту. Через 24 год від початку розвитку запалення ефект від застосування екстракту був дещо нижчим. Але найменш виражений його вплив на розвиток запалення відзначали через 1 год дослідження. Аналогічний вплив мав диклофенак натрію, щоправда значний ефект від його застосування проявився вже через 1 год від початку експерименту.

Висновок. Доведено виразну протизапальну активність сухого екстракту з листя салату посівного, який найбільш активно пригнічує розвиток набряку лапи щурів через 1 год запалення.
Visual Simultaneity Judgments Activate a Bilateral Frontoparietal Timing System
Authors: Hanayik Taylor , Yourganov Grigori , Newman-Norlund Roger , Gibson Makayla , Rorden Chris
Published: November 2018

In everyday life, we often make judgments regarding the sequence of events, for example, deciding whether a baseball runner's foot hit the plate before or after the ball hit the glove. Numerous studies have examined the functional correlates of temporal processing using variations of the temporal order judgment and simultaneity judgment (SJ) tasks. To perform temporal order judgment tasks, observers must bind temporal information with identity and/or spatial information relevant to the task itself. SJs, on the other hand, require observers to detect stimulus asynchrony but not the order of stimulus presentation and represent a purer measure of temporal processing. Some previous studies suggest that these temporal decisions rely primarily on right-hemisphere parietal structures, whereas others provide evidence that temporal perception depends on bilateral TPJ or inferior frontal regions (inferior frontal gyrus). Here, we report brain activity elicited by a visual SJ task. Our methods are unique given our use of two orthogonal control conditions, discrimination of spatial orientation and color, which were used to control for brain activation associated with the classic dorsal (“where/how”) and ventral (“what”) visual pathways. Our neuroimaging experiment shows that performing the SJ task selectively activated a bilateral network in the parietal (TPJ) and frontal (inferior frontal gyrus) cortices. We argue that SJ tasks are a purer measure of temporal perception because they do not require observers to process either identity or spatial information, both of which may activate separate cognitive networks.
Disentangling Neural Sources of Problem Size and Interference Effects in Multiplication
Authors: Tiberghien Kerensa , Sahan Muhammet I. , De Smedt Bert , Fias Wim , Lyons Ian M.
Published: November 2018

Multiplication is thought to be primarily solved via direct retrieval from memory. Two of the main factors known to influence the retrieval of multiplication facts are problem size and interference. Because these factors are often intertwined, we sought to investigate the unique influences of problem size and interference on both performance and neural responses during multiplication fact retrieval in healthy adults. Behavioral results showed that both problem size and interference explained separate unique portions of RT variance, but with significantly stronger contribution from problem size, which contrasts with previous work in children. Whole-brain fMRI results relying on a paradigm that isolated multiplication fact retrieval from response selection showed highly overlapping brain areas parametrically modulated by both problem size and interference in a large network of frontal, parietal, and subcortical brain areas. Subsequent analysis within these regions revealed problem size to be the stronger and more consistent “unique” modulating factor in overlapping regions as well as those that appeared to respond only to problem size or interference at the whole-brain level, thus underscoring the need to look beyond anatomical overlap using arbitrary thresholds. Additional unique contributions of interference (beyond problem size) were identified in right angular gyrus and subcortical regions associated with procedural processing. Together, our results suggest that problem size, relative to interference, tends to be the more dominant factor in driving behavioral and neural responses during multiplication fact retrieval in adults. Nevertheless, unique contributions of both factors demonstrate the importance of considering the overlapping and unique contributions of each in explaining the cognitive and neural bases of mental multiplication.
First record of the assassin bug subfamily Centrocnemidinae (Hemiptera: Heteroptera: Reduviidae) from Vietnam, with the description of a new species
Authors: TRUONG XUAN LAM , LI HU , CAI WANZHI
Published: November 2018

The reduviid subfamily Centrocnemidinae is reported from Vietnam for the first time, with a new species, Centrocnemis schaeferi Truong, Li & Cai. The new species is distinguished from other members of the genus Centrocnemis by the black spots and confluent suffusions on the posterior pronotal lobe, the rostrum and the membrane of forewings, and whitish tubercles on the apical and basal potions of the corium.
Three new species of Benedenia Diesing, 1858 from the Great Barrier Reef, Australia with a key to species of the genus
Authors: DEVENEY MARTY R. , WHITTINGTON IAN D.
Published: November 2018

Three new species of Benedenia are described from the Great Barrier Reef: B. ernsti n. sp., B. fieldsi n. sp. and B. haywardi n. sp. Allobenedenia ishikawae (Goto, 1894) Yamaguti, 1963 does not fit the diagnosis of Allobenedenia Yamaguti, 1963 as amended by Yang, Kritsky & Sun, 2004 and we return it to Benedenia as B. ishikawae (Goto, 1894) Monticelli, 1902. We consider Benedenia sargocentron Zhang, Yang & Liu, 2001 a synonym of B. hawaiiensis. Benedenia now consists of 25 species with a broad range of morphological variations, host relationships and microhabitats. A key to species of Benedenia is presented. Benedenia fieldsi may pose a significant risk to sea cage aquaculture of its serranid hosts.
Two new nematode species of the genus Cosmocephalus Molin, 1858 (Spirurida: Acuariidae), with an amended generic diagnosis and an identification key to Cosmocephalus spp.
Authors: MUTAFCHIEV YASEN , HALAJIAN ALI , GEORGIEV BOYKO B.
Published: November 2018

Cosmocephalus podicipis n. sp. is described from Podiceps cristatus from the vicinity of Ramsar, Iran (type host and type locality) and from Podiceps nigricollis from the Bulgarian Black Sea coast. Cosmocephalus pelecani n. sp. is described from Pelecanus conspicillatus from Mansfield, Victoria, Australia. Comparative materials of three other species of Cosmocephalus were examined and described. These are C. obvelatus (based on specimens from Larus argentatus from Bulgaria), C. jaenschi (based on a paratype from Phalacrocorax carbo from Australia) and C. capellae (based on a male nematode from Tringa totanus from Bulgaria, a new geographical record). Cosmocephalus faridi from Pelecanus onocrotalus from Egypt, which has been considered by previous authors as a synonym of C. obvelatus, is validated. Results of SEM observations are presented for C. podicipis and C. obvelatus. In all the species examined, the presence of a single ventral ridge was recorded in males anterior to the caudal bursa. The generic diagnosis is amended to include more comprehensive information on the morphology of the studied species. Currently, the genus Cosmocephalus includes 7 species. Cosmocephalus imperialis is recognised as a species inquirenda. Cosmocephalus argentinensis is proposed as a junior synonym of C. obvelatus. An identification key to the species of Cosmocephalus is presented.
A new species of Hyphessobrycon (Teleostei: Characiformes: Characidae) from the San Juan River drainage, Pacific versant of Colombia
Authors: GARCÍA–ALZATE CARLOS A. , ROMÁN–VALENCIA CÉSAR , TAPHORN DONALD C.
Published: November 2018

We describe a new species, Hyphessobrycon sebastiani, from the San Juan River drainage of the Pacific versant of Colombia. This new species of Hyphessobrycon is distinguished from all congeners that share two humeral spots and no caudal blotch by having: five unbranched and 25 to 28 branched anal–fin rays; 12–13 branched pectoral–fin rays; 35–37 scales in the longitudinal series; eight scales between the lateral line and the dorsal–fin origin; 12–13 predorsal scales; 13–18 pored lateral–line scales and three pairs of large bony hooks on anal fin of mature males.
On the occurrence of the genus Paranebalia (Crustacea: Phyllocarida: Leptostraca) in northern Patagonia, Argentina
Authors: ROCCATAGLIATA DANIEL , CHIESA IGNACIO L. , RAFFO M. PAULA , SIMES ELENA GÓMEZ
Published: November 2018

In the present study, the genus Paranebalia is recorded from Argentina for the first time, with a large number of specimens collected in Nuevo, San José and San Matías Gulfs, northern Patagonia, in the years 2003 to 2007 (see Fig. 1). Although these specimens agree with the diagnostic characters of Paranebalia longipes (Willemöes-Suhm, 1875), the description and subsequent redescriptions of this species are not sufficiently detailed for a reliable identification. Hence, we provisionally named our material as Paranebalia cf. longipes (see below).
A General Method for Estimating Bulk 2D Projections of Ice Particle Shape: Theory and Applications
Authors: Dunnavan Edwin L. , Jiang Zhiyuan
Published: November 2018

The orientation of falling ice particles directly influences estimates of microphysical and radiative bulk quantities as well as in situ retrievals of size, shape, and mass. However, retrieval efforts and bulk calculations often incorporate very basic orientations or ignore these effects altogether. To address this deficiency, this study develops a general method for projecting bulk distributions of particle shape for arbitrary orientations. The Amoroso distribution provides the most general bulk aspect ratio distribution for gamma-distributed particle axis lengths. The parameters that govern the behavior of this aspect ratio distribution depend on the assumed relationship between mass, maximum dimension, and aspect ratio. Individual spheroidal geometry allows for eccentricity quantities to linearly map onto ellipse analogs, whereas aspect ratio quantities map nonlinearly. For particles viewed from their side, this analytic distinction leads to substantially larger errors in projected aspect ratio than for projected eccentricity. Distribution transformations using these mapping equations and numerical integration of projection kernels show that both truncation of size distributions and changes in Gaussian dispersion can alter the modality and shape of projection distributions. As a result, the projection process can more than triple the relative entropy between the spheroidal and projection distributions for commonly assumed model and orientation parameters. This shape uncertainty is maximized for distributions of highly eccentric particles and for particles like aggregates that are thought to fall with large canting-angle deviations. As a result, the methods used to report projected aspect ratios and the corresponding values should be questioned.
Congenital tuberculosis after in vitro fertilization: suggestion for tuberculosis tests in infertile women in developing countries
Authors: Zhang Xiaoling , Zhuxiao Ren , Xu Fang , Zhang Qi , Yang Haoming , Chen Liang , Liu Fenghua , Yang Jie
Published: November 2018

Congenital tuberculosis (CTB) after in vitro fertilization (IVF) is a major new problem in developing countries. Only 16 cases of CTB after IVF have been reported, and no tuberculosis (TB) tests were performed before IVF in these cases. However, on the basis of data in the literature and from the World Health Organization, the incidence of CTB has been substantially underestimated. We describe two cases of CTB after IVF in detail in our center and provide new insight into the important issue of controlling TB vertical transmission in developing countries. Performing an early diagnosis of CTB, mostly based on evidence of maternal infection and a high index of clinical suspicion, is a challenge. However, most mothers have no symptoms of TB infection during prepartum, and infertility may be the only symptom. Infertility caused by genital TB is common in countries with a high TB burden, and IVF is considered to be an effective treatment to improve their fertility. Therefore, this may lead to more CTB cases without thorough TB tests before IVF. We suggest that thorough TB tests should be conducted in infertile women before IVF to prevent CTB.
A Menu-driven Facility for Complex Sample Size Calculation in Randomized Controlled Trials with a Survival or a Binary Outcome
Authors: Royston Patrick , Babiker Abdel
Published: November 2018

We present a menu-driven Stata program for the calculation of sample size or power for complex clinical trials with a survival time or a binary outcome. The features supported include up to six treatment arms, an arbitrary time-to-event distribution, fixed or time-varying hazard ratios, unequal patient allocation, loss to follow-up, staggered patient entry, and crossover of patients from their allocated treatment to an alternative treatment. The computations of sample size and power are based on the logrank test and are done according to the asymptotic distribution of the logrank test statistic, adjusted appropriately for the design features.
Review of Statistics with Stata (Updated for Version 7)
Authors: Freese Jeremy
Published: November 2018

The new book by Hamilton (2002) is reviewed.
Review of Statistical Modeling for Biomedical Researchers by Dupont
Authors: Garrett Joanne M.
Published: November 2018

The new book by Dupont (2002) is reviewed.
Review of Generalized Latent Variable Modeling by Skrondal and Rabe-Hesketh
Authors: Newson Roger
Published: November 2018

The new book by Skrondal and Rabe-Hesketh (2004) is reviewed.
Using the File Command to Produce Formatted Output for other Applications
Authors: Slaymaker Emma
Published: November 2018

The file command provides a way to produce tables for use in other application software. It can be especially useful for combining descriptive results (such as means and percentages) and results from significance tests. Extracting and manipulating the results directly from Stata matrices gives more control over arrangement, while other Stata functions may be used to control numeric formats. This tutorial includes examples based on survey data of both plain text and HTML output.
Tests and Confidence Sets with Correct Size when Instruments are Potentially Weak
Authors: Mikusheva Anna , Poi Brian P.
Published: November 2018

We consider inference in the linear regression model with one endogenous variable and potentially weak instruments. We construct confidence sets for the coefficient on the endogenous variable by inverting the Anderson–Rubin, Lagrange multiplier, and conditional likelihood-ratio tests. Our confidence sets have correct coverage probabilities even when the instruments are weak. We propose a numerically simple algorithm for finding these confidence sets, and we present a Stata command that supersedes the one presented in Moreira and Poi ( Stata Journal 3: 57–70).
Speaking Stata: Making it Count
Authors: Cox Nicholas J.
Published: November 2018

The count command has one simple role, to count observations in general or that satisfy some condition(s). This task can be useful when some larger problem pivots on counting, especially if count is used with a loop over observations or variables. I use various problems, mostly of data management, as examples. I also make comparisons with the use of _N, summarize, and egen for the same or similar problems.
Speaking Stata: Paired, Parallel, or Profile Plots for Changes, Correlations, and Other Comparisons
Authors: Cox Nicholas J.
Published: November 2018

Paired, parallel, or profile plots showing the values of two variables may be constructed readily using a combination of graph twoway commands. This column explores the principles and practice of such plot-making, considering both wide and long (panel or longitudinal) data structures in which such data may appear. Applications include analysis of change over time or space and indeed any kind of correlation or comparison between variables. Such plots may be extended to show numeric values and associated name information.
Respondent-Driven Sampling
Authors: Schonlau Matthias , Liebau Elisabeth
Published: November 2018

Respondent-driven sampling is a network sampling technique typically employed for hard-to-reach populations (for example, drug users, men who have sex with men, people with HIV). Similarly to snowball sampling, initial seed respondents recruit additional respondents from their network of friends. The recruiting process repeats iteratively, thereby forming long referral chains. Unlike in snowball sampling, it is crucial to obtain estimates of respondents’ personal network sizes (that is, number of acquaintances in the target population) and information about who recruited whom. Markov chain theory makes it possible to derive population estimates and sampling weights. We introduce a new Stata command for respondent-driven sampling and illustrate its use.
Long-Run Covariance and its Applications in Cointegration Regression
Authors: Wang Qunyong , Wu Na
Published: November 2018

Long-run covariance plays a major role in much of time-series inference, such as heteroskedasticity- and autocorrelation-consistent standard errors, generalized method of moments estimation, and cointegration regression. We propose a Stata command, lrcov, to compute long-run covariance with a prewhitening strategy and various kernel functions. We illustrate how long-run covariance matrix estimation can be used to obtain heteroskedasticity- and autocorrelation-consistent standard errors via the new hacreg command; we also illustrate cointegration regression with the new cointreg command. hacreg has several improvements compared with the official newey command, such as more kernel functions, automatic determination of the lag order, and prewhitening of the data. cointreg enables the estimation of cointegration regression using fully modified ordinary least squares, dynamic ordinary least squares, and canonical cointegration regression methods. We use several classical examples to demonstrate the use of these commands.
Two-stage Individual Participant Data Meta-analysis and Generalized Forest Plots
Authors: Fisher David J.
Published: November 2018

In this article, I describe a command, ipdmetan, that facilitates two-stage individual participant data meta-analysis of any measure of effect and its standard error by fitting a specified model to data from each study. The command can estimate random effects and heterogeneity statistics and include additional covariates and interactions. If individual participant data are available for certain studies and aggregate data for others, ipdmetan allows them to be combined in one analysis. This command can produce detailed and flexible forest plots, including ones outside the context of formal meta-analysis.
Features of the Area under the Receiver Operating Characteristic (ROC) Curve. A Good Practice
Authors: Lora David , Contador Israel , Pérez-Regadera José F. , de la Cámara Agustín Gómez
Published: November 2018

The area under the receiver operating characteristic (ROC) curve is a measure of discrimination ability used in diagnostic and prognostic research. The ROC plot is usually represented without additional information about decision thresholds used to generate the graph. In our article, we show that adding at least one or more informative cutoff points on the ROC graph facilitates the characterization of the test and the evaluation of the discriminatory capacities, which can result in more informed medical decisions. We use the rocreg and rocregplot commands.
Calculate Travel Time and Distance with Openstreetmap Data Using the Open Source Routing Machine (OSRM)
Authors: Huber Stephan , Rust Christoph
Published: November 2018

In this article, we introduce the osrmtime command, which calculates the distance and travel time between two points using latitude and longitude information. The command uses the Open Source Routing Machine (OSRM) and OpenStreetMap to find the optimal route by car, by bicycle, or on foot. The procedure is specially built for large georeferenced datasets. Because it is fast, the command uses the full computational capacity of a PC, allows the user to make unlimited requests, and is independent of the Internet and commercial online providers. Hence, there is no risk of the command becoming obsolete. Moreover, the results can be replicated at any time.
A Generalized Regression-adjustment Estimator for Average Treatment Effects from Panel Data
Authors: Drukker David M.
Published: November 2018

I illustrate that the simple regression-adjustment estimator is inconsistent for the average treatment effect when the random effects affecting treatment assignment are correlated with the random effects that affect the potential outcomes. I present a simple parametric estimator that is consistent in this case.