bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the wonders of replication
Authors: Klevjer Kristoffer 
Published: October 2019

The lack of replicating research is not new, still the recent "replication crisis" has made a large impact in the social and life sciences which subsequently increased their replication efforts. Most scholars do agree on the need for solid, preregistered, direct replications. However, performing them is less common, after all, researchers have their own ideas! Underestimated is though, that replications are beneficial for science, the students and supervisors!
As a part of my master's thesis I performed a direct replication – and this turned into one of the most educational parts of my whole psychology degree. It was an excellent introduction to the importance of a solid method section, to Open Science and preregistration.

It changed the way I read and evaluate articles.
I learned the distinction between confirmatory and exploratory hypotheses.
It highlighted the need for strict adherence to data collection protocols.
It taught me the publishing process in a nutshell by starting data collection only after my protocol and procedures was approved by external researchers.

I argue that replication are beneficial for supervisors too.

Students get a thorough introduction to said concepts, which increases confidence in their work (ethics) and trust in science.
Replications are time-effective alternatives for bachelors students.
Supervisors can exchange ideas with other supervisors as well as use this for networking

In sum, science needs it, students like and learn from it, and it is convenient and helpful for supervisors. Next time: please pitch a replication project to your student!
Soil bacterial biodiversity is driven by long-term pasture management, poultry litter, and cattle manure inputs
Authors: Yang Yichao , Ashworth Amanda J. , DeBruyn Jennifer M. , Willett Cammy , Durso Lisa M. , Cook Kim , Moore, Jr. Philip A. , Owens Phillip R. 
Published: October 2019

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.
Smart Vehicle Tracking System through IoT
Authors: Sriashalya S. , Kalyani Y. 
Published: September 2019

This study evaluates the importance of connecting objects through the concept of the Internet of things (IoT). There has been an increasing trend in the topic of the Internet of Things in various sectors. Almost all, such as area, devices, the software is connected which all can be accessed remotely or virtually through smart devices. The most typical invention is the smartphone which that acts like the computer and sometimes even smatter smarter when connected with web & internet. But the new term smart homes where all the devices and machinery are connected to ensure that all smart processes are smart. This can be extended to a smart village, smart city and smart industry. Here we introduce a vehicle tracking system by using the concept IoT. Message Queuing Telemetry Transport (MQTT) is a protocol commonly used in the IoT platform to share information. It can be used for both publishings and subscribe subscribing data from one end to another. Here we have used the same technique has been used in the present work to design a simulation to track the exact location of a given vehicle. IOT broker and the smart devices were integrated into the middleware enterprise service bus the middleware (ESB) architecture and the simulation was run with numerous geolocations.
Evaluation of in vitro Antioxidant Activities of Ethanol Extracts of Datura innoxia Mill. Leaves and Seeds Harvested in Mali
Authors: Togola Issiaka , Dembélé Abdramane Ansoumany , Tounkara Fatoumata , Diarra Nouhoum , Konaré Mamadou Abdoulaye , Karembé Moussa , Maïga Seydou Zibba , Dembélé Doulaye 
Published: September 2019

Aims: The purpose of this study was to evaluate the in vitro antioxidant activities of Datura innoxia Mill. leaves and seeds harvested in Mali.
Place and Duration of Study: Collection of plant materials were done at Kolondieba (Mali) in june 2016. Evaluation of polyphenols and flavonoids contents, determination of antioxidant activities were done at Laboratory of Plant and Food Biochemistry and Biotechnology of University of Sciences, Techniques and Technologies of Bamako (Mali) between august 2016 and March 2017.
Methodology: The leaves and seeds were collected in Kolondieba, Mali. The phytochemical screening based on the standard methods of tube reactions has been performed with ethanol extracts. The quantitative estimation of total polyphenols was made by the Folin-Ciocalteu method and that of flavonoids by the use of aluminum trichloride. The in vitro antioxidant activities of the ethanol extracts was determined by three methods: the 1,1- diphenyl - 2- picrylhydrazyl (DPPH) test, the ferric reducing ability power (FRAP) test and the Phosphomolybdate test (PPM).
Results: The phytochemical screening revealed that leaves and seeds of this plant contains alkaloids, polyphenols, flavonoids, coumarins, tannins, triterpenes and saponin. Phenolic contents of ethanol extracts are 30.97 ± 0.33 mg equivalent gallic acid / g in leaves and 14.02 ± 0.15 mg equivalent gallic acid / g in seeds; those of flavonoids are 15.13 ± 0.2 mg equivalent of quercetin / g in the leaves and 4.93 ± 0.41 mg equivalent of quercetin / g in the seeds. The three tests showed that the leaves have a higher level of antiradical activity in vitro than seeds.
Conclusion: The results of this work showed that Datura innoxia Mill. has a good antioxidant activity which would justify its use as a potential source of natural antioxidants.
Inhibitory Effect of Dry Garlic Powder on the Nickel Chloride-induced Somatic and Germinal Cell Damages in Male Mice
Authors: Rabbani Syed Imam 
Published: October 2019

Background: Nickel is commonly used in industry, utensils and also present in cigarette. Over-exposure of nickel is known to cause several health complications including somatic and germinal cell injuries. Garlic (Allium sativum) being a spice has several pharmacological properties. However, its role on the nickel chloride induced somatic and reproductive cells damages are poorly studied in the literature.
Objective: To evaluate the effect of garlic powder on nickel chloride induced somatic and germinal cell damages in male mice.
Methods: Dried garlic clove powder is used in this study in three doses via., 50. 100 and 150 mg/kg, per oral (p.o) for 4-weeks against the nickel chloride [(10 mg/kg, intraperitoneal (i.p)] induced somatic and germinal damages. Somatic cells damages were studied using peripheral micronucleus test and germinal cell damages by sperm count and sperm shape abnormalities in male mice. Further, the in-vitro hydrogen peroxide scavenging activity of the garlic was evaluated. Ascorbic acid was tested as a standard drug. The data of the results were analyzed by One-way Anova and Tukey as post hoc test.
Results: The result indicated that nickel chloride enhanced significantly (p<0.001) both somatic and germinal cell damages compared to control animals. The administration of garlic powder at 150 mg/kg significantly (p<0.001) minimized the frequency of micronuclei in the erythrocytes and reduced the spermatozoa anomalies compared to the nickel chloride group. The garlic powder also exhibited significant hydrogen peroxide scavenging activity.
Conclusion: The data indicated that garlic powder at 150 mg/kg reduced the cellular damaging effects of nickel chloride on somatic and germinal cells and the mechanism could be related to the free radical scavenging activity.
Common age‐related neuropathologies and yearly variability in cognition
Authors: Yu Lei , Wang Tianhao , Wilson Robert S. , Leurgans Sue , Schneider Julie A. , Bennett David A. , Boyle Patricia A. 
Published: October 2019

AbstractObjectiveCognitive variability is a potentially important source of heterogeneity in longitudinal cognitive profiles. We examined the extent to which common age‐related neuropathologies including Lewy bodies and Alzheimer’s disease (AD) contribute to yearly variability in late life cognition.MethodsData came from 1321 community‐dwelling older adults who were followed annually for up to 23 years, died and underwent brain autopsy. Cognition was assessed via a comprehensive testing battery. Uniform neuropathologic evaluations assessed burdens of Lewy bodies, AD, infarcts, TDP, hippocampal sclerosis, amyloid angiopathy, atherosclerosis, and arteriolosclerosis. Using mixed effects models, yearly variability in cognition, characterized as within‐person variability of annual cognitive scores, was regressed on the nine neuropathologic indices.ResultsThe average age of decedents was 90 years and 69% were female. At autopsy, about two thirds met the pathologic criteria for AD. Neocortical Lewy bodies were present in 13% of the individuals. Other neuropathologic conditions also were common. All neuropathologic indices except for microinfarcts were associated with cognitive decline. Individuals with neocortical Lewy bodies had almost twice the yearly variability in cognition compared to those without. Individuals with AD had about 70% more variability compared to those without. Yearly variability was present among persons with vascular diseases but to a lesser degree than neocortical Lewy bodies and AD.InterpretationLewy body pathology is associated with pronounced variability in annual cognitive assessments but this finding is not unique to this pathology. Comparable variability is present among persons with AD pathology and to a lesser extent among persons with cerebrovascular pathologies.
Progressive familial intrahepatic cholestasis type‐3 and multiple sclerosis: lessons from comorbidity
Authors: De Masi Roberto , Orlando Stefania , De Donno Antonella 
Published: October 2019

AbstractThe comorbidity between multiple sclerosis (MS) and progressive familial intrahepatic cholestasis type‐3 (PFIC3) has never been described yet. ABCB4 gene encodes the multidrug resistant protein 3 (MDR3) and its mutations induce PFIC3 as well as intrahepatic cholestasis of pregnancy (ICP) and drug‐induced liver injury (DILI). We describe the case of a 32‐year‐old female with MS and PFIC3 who was effectively treated with natalizumab and ursodeoxycholic acid (UCDA), in contrast to glatiramer acetate, dimethylfumarate, and IFNb1a associated with DILI. Our findings clarify the pharmacodynamics of MS therapies and suggest natalizumab plus UDCA as the effective treatment of PFIC3/MS phenotype, unlike the others that should be avoided.
Quantum Materials with Atomic Precision: Artificial Atoms in Solids: Ab Initio Design, Control, and Integration of Single Photon Emitters in Artificial Quantum Materials
Authors: Narang Prineha , Ciccarino Christopher J. , Flick Johannes , Englund Dirk 
Published: October 2019

AbstractThis Progress Report explores advances and opportunities in the atomic‐scale design, fabrication, and imaging of quantum materials toward creating artificial atoms in solids with tailored optoelectronic and quantum properties. The authors outline an “ab initio” approach to quantitatively linking first‐principles calculations and atomic imaging with atomic patterning, setting the stage for new designer quantum nanomaterials.
Smart Stretchable Janus Membranes with Tunable Collection Rate for Fog Harvesting
Authors: Su Yahui , Cai Shengwen , Wu Tao , Li Chuanzong , Huang Zhouchen , Zhang Yiyuan , Wu Hao , Hu Kai , Chen Chao , Li Jiawen , Hu Yanlei , Zhu Suwan , Wu Dong 
Published: October 2019

AbstractWater scarcity is one of the severest global resource shortages because freshwater plays a vital role in human existence. Fog harvesting is a promising approach to alleviate freshwater shortage, but most existing strategies based on rigid materials suffer from the shortage of nontunable fog collection rate. Herein, a smart Janus membrane with a tunable fog collection rate via uniaxially stretching a flexible polydimethylsiloxane sheet fabricated by ultrafast laser drilling is reported. Compared to its original form, the maximum strain of 200% shows up to 67% enhancement in its fog collection efficiency. Further theoretical calculation demonstrates that the increase of fog collection rate along with uniaxially stretching is estimated to be ≈79% for 200% strain sample based on the cooperation between the wetting driving force and Laplace pressure, which is in well agreement with the experimental result. It is believed that this smart Janus membrane would operate not only in the field of fog harvesting, but also in specific scenarios, such as dynamic fog‐flux regulators.
A Shift in Porcine Circovirus 3 (PCV‐3) History Paradigm: Phylodynamic Analyses Reveal an Ancient Origin and Prolonged Undetected Circulation in the Worldwide Swine Population
Authors: Franzo Giovanni , He Wanting , Correa‐Fiz Florencia , Li Gairu , Legnardi Matteo , Su Shuo , Segalés Joaquim 
Published: October 2019

AbstractThe identification of a new circovirus (Porcine circovirus 3, PCV‐3) has raised a remarkable concern because of some analogies with Porcine circovirus 2 (PCV‐2). Preliminary results suggest an extremely recent PCV‐3 emergence and high mutation rate. Retrospective studies prove its circulation at least since the early 1990s, revealing that PCV‐3 could have been infecting pigs for an even longer period. Therefore, a new evaluation, based on an updated collection of PCV‐3 sequences spanning more than 20 years, is performed using a phylodynamic approach. The obtained results overrule the previous PCV‐3 history concept, indicating an ancient origin. These evidences are associated with an evolutionary rate far lower (10−5–10−6 substitution/site/year) than the PCV‐2 one. Accordingly, the action of selective pressures on PCV‐3 open reading frames (ORFs) seems to be remarkably lower compared to those acting on PCV‐2, suggesting either a reduced PCV‐3 plasticity or a less efficient host‐induced natural selection. A complex and not‐directional viral flow network is evidenced through phylogeographic analysis, indicating a long lasting circulation rather than a recent emergence followed by spreading. Being recent emergence has been ruled out, efforts should be devoted to understand whether its recent discovery is simply due to improved detection capabilities or to the breaking of a previous equilibrium.
Body fat percent assessment between electrical impedance myography and dual X‐ray absorptiometry
Authors: Czeck Madeline A. , Raymond‐Pope Christiana J. , Prescott Elyse , Bisch Katie L. , Dengel Donald R. 
Published: October 2019

AbstractObjectivesTo compare total and regional body fat percent (BF%) measurements obtained using a handheld electrical impedance myography (EIM) device in comparison to BF% measured by dual X‐ray absorptiometry (DXA).MethodsSixty‐nine male and female (33 males/36 females; age = 21.9 ± 2.0 years, body mass index = 24.5 ± 3.6 kg/m2) college‐age individuals participated in this study. Each participant's total and regional (ie, upper arms, upper legs, trunk) BF% was estimated using EIM and DXA. Metallic markers were used to delineate regional boundaries for analysis, including upper arms (biceps/triceps), upper legs (quadriceps/hamstrings), and trunk (abdominal region/low back region). Paired t‐tests assessed the accuracy of BF% values estimated from EIM in comparison to BF% measured by DXA.ResultsObservations revealed EIM reported significantly lower BF% for upper left arm (P < .001), upper right arm (P < .001), upper right leg (P = .002), and trunk (P < .001) values. However, no significant differences were observed in total (P = .434) and upper left leg (P = .855) BF% between the two devices.ConclusionsThis study's observations suggest that, EIM may be an accurate field method for measuring total BF%, but not regional BF%.
Trisomy 13 and 18—Prevalence and mortality—A multi‐registry population based analysis
Authors: Goel Nitin , Morris Joan K. , Tucker David , de Walle Hermien E. K. , Bakker Marian K. , Kancherla Vijaya , Marengo Lisa , Canfield Mark A. , Kallen Karin , Lelong Nathalie , Camelo Jorge L. , Stallings Erin B. , Jones Abbey M. , Nance Amy , Huynh My‐Phuong , Martínez‐Fernández Maria‐Luisa , Sipek Antonin , Pierini Anna , Nembhard Wendy N. , Goetz Dorit , Rissmann Anke , Groisman Boris , Luna‐Muñoz Leonora , Szabova Elena , Lapchenko Serhiy , Zarante Ignacio , Hurtado‐Villa Paula , Martinez Laura E. , Tagliabue Giovanna , Landau Danielle , Gatt Miriam , Dastgiri Saeed , Morgan Margery 
Published: October 2019

AbstractThe aim of the study is to determine the prevalence, outcomes, and survival (among live births [LB]), in pregnancies diagnosed with trisomy 13 (T13) and 18 (T18), by congenital anomaly register and region. Twenty‐four population‐ and hospital‐based birth defects surveillance registers from 18 countries, contributed data on T13 and T18 between 1974 and 2014 using a common data‐reporting protocol. The mean total birth prevalence (i.e., LB, stillbirths, and elective termination of pregnancy for fetal anomalies [ETOPFA]) in the registers with ETOPFA (n= 15) for T13 was 1.68 (95% CI 1.3–2.06), and for T18 was 4.08 (95% CI 3.01–5.15), per 10,000 births. The prevalence varied among the various registers. The mean prevalence among LB in all registers for T13 was 0.55 (95%CI 0.38–0.72), and for T18 was 1.07 (95% CI 0.77–1.38), per 10,000 births. The median mortality in the first week of life was 48% for T13 and 42% for T18, across all registers, half of which occurred on the first day of life. Across 16 registers with complete 1‐year follow‐up, mortality in first year of life was 87% for T13 and 88% for T18. This study provides an international perspective on prevalence and mortality of T13 and T18. Overall outcomes and survival among LB were poor with about half of live born infants not surviving first week of life; nevertheless about 10% survived the first year of life. Prevalence and outcomes varied by country and termination policies. The study highlights the variation in screening, data collection, and reporting practices for these conditions.
Baseline cortisol levels and social behavior differ as a function of handedness in marmosets (Callithrix jacchus)
Authors: Vaughan Emma , Le Annie , Casey Michaela , Workman Kathryn P. , Lacreuse Agnès 
Published: October 2019

AbstractPopulation hand preferences are rare in nonhuman primates, but individual hand preferences are consistent over a lifetime and considered to reflect an individual's preference to use a particular hemisphere when engaged in a specific task. Previous findings in marmosets have indicated that left‐handed individuals tend to be more fearful than their right‐handed counterparts. Based on these findings, we tested the hypotheses that left‐handed marmosets are (a) more reactive to a social stressor and (b) are slower than right‐handed marmosets in acquiring a reversal learning task. We examined the hand preference of 27 male and female marmosets (ages of 4–7 years old) previously tested in a social separation task and a reversal learning task. Hand preference was determined via a simple reaching task. In the social separation task, monkeys were separated from their partner and the colony for a single 7‐hr session. Urinary cortisol levels and behavior were assessed at baseline, during the separation and 24 hr postseparation. Hand preferences were equally distributed between left (n = 10), right‐handed (n = 10), and ambidextrous (n = 7) individuals. The separation phase was associated with an increase in cortisol levels and behavioral changes that were similar across handedness groups. However, cortisol levels at baseline were positively correlated with right‐handedness, and this relationship was stronger in females than in males. In addition, the occurrence of social behaviors (pre‐ and postseparation) was positively correlated with right‐handedness in both sexes. Baseline cortisol levels did not correlate significantly with social behavior. Acquisition of the reversals was poorer in females than males but did not differ as a function of handedness. We conclude that (a) both stress reactivity and cognitive flexibility are similar across handedness groups and (b) left‐handers exhibit less social behavior and have lower basal cortisol levels than ambidextrous and right‐handed subjects. The underlying causes for these differences remain to be established.
Multiple Oscillatory Push–Pull Antagonisms Constrain Seizure Propagation
Authors: Jiang Haiteng , Cai Zhengxiang , Worrell Gregory A. , He Bin 
Published: October 2019

ObjectiveDrug‐resistant focal epilepsy is widely recognized as a network disease in which epileptic seizure propagation is likely coordinated by different neuronal oscillations such as low‐frequency activity (LFA), high‐frequency activity (HFA), or low‐to‐high cross‐frequency coupling. However, the mechanism by which different oscillatory networks constrain the propagation of focal seizures remains unclear.MethodsWe studied focal epilepsy patients with invasive electrocorticography (ECoG) recordings and compared multilayer directional network interactions between focal seizures either with or without secondary generalization. Within‐frequency and cross‐frequency directional connectivity were estimated by an adaptive directed transfer function and cross‐frequency directionality, respectively.ResultsIn the within‐frequency epileptic network, we found that the seizure onset zone (SOZ) always sent stronger information flow to the surrounding regions, and secondary generalization was accompanied by weaker information flow in the LFA from the surrounding regions to SOZ. In the cross‐frequency epileptic network, secondary generalization was associated with either decreased information flow from surrounding regions’ HFA to SOZ's LFA or increased information flow from SOZ's LFA to surrounding regions’ HFA.InterpretationOur results suggest that the secondary generalization of focal seizures is regulated by numerous within‐ and cross‐frequency push–pull dynamics, potentially reflecting impaired excitation–inhibition interactions of the epileptic network. ANN NEUROL 2019;86:683–694