bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of Higher Order Thinking Skills in Genetic Learning: A Validity, Practicality, and Reliability
Authors: Marlina D I , Rahmi Y L
Published: June 2021

The ability of higher order thinking skills students in West Sumatra is still low relatively with an average value in the range of 17.88-38.45. This is evidenced by the existence of trial tests at schools in several areas in West Sumatra. One way to improve the level of thinking ability of students is to develop assessment of higher order thinking skills. This research aims to develop instruments of higher order thinking skills about genetic material that is valid, practical and reliable. This study uses a 4-D models development. The subjects of this study were two biology lecturers from Faculty of Mathematics and Science, Universitas Negeri Padang, two biology teachers and 30 students of class XII SMAN 1 Nan Sabaris. Data were collected by using questionnaire for validity and practicality furthermore for getting value of reliability by using test. Based on data analysis, the value of validity, practicality, and reliability obtained an average of 87.72%, 88.54% and 0,80 respectively. In a nut shell, the instruments which is designed has been valid, practical and reliable, which can be used by teachers to measure and foster students’ of higher-order thinking skills.
A Contextual Biodiversity Handbook to Identify Bintan Coastal Invertebrates
Authors: Amelia Trisna , Sarkawi  , Irawan Bony
Published: June 2021

Contextual teaching and learning is quite important to be applied due to students weakness in connecting between what they learn and how the knowledge will be used. It is a learning system that matches the performance of the brain, to construct patterns that embody meaning, by linking the academic content with the context of learners’ everyday life. By applying contextual teaching and learning the information received is not only stored in short-term memory, which is easily forgotten, but can be stored in long-term memory. Contextual teaching and learning can be applied through various learning components. One of them is by applying appropriate learning resources/learning media to facilitate contextual learning. Through research and development applying Plomp model, a handbook has been developed to identify specific invertebrates exist on the coast of Bintan (the Province of Kepulauan Riau). This handbook was developed through processes namely; (1) collecting invertebrates of the coastal area of Bintan, (2) identifying invertebrates using research publications, (3) displaying content in the form of handbooks applying attractive designs, (4) suggestions for improvements by validators, and (5) test the feasibility through trials in learning. These processes drive the handbook different from most learning resources on this topic that do not specifically provide information about invertebrates exist in Bintan or Kepulauan Riau. The using of handbook encourages 100% completeness in learning mastering for 21 students. Furthermore, it increases learning motivation in a high increasing category.
Development of Bioremediation Learning Materials based on Contextual Teaching and Learning (CTL)
Authors: Astuti Y , Ahda Y , Putri D H
Published: June 2021

Structured learning materials function as ground base for students to read and analyze topic related on deeper level. This succession in learning emerge as a problem in biotechnology course for bioremediation topic at Biology Education Department of Universitas Negeri Padang. Students had to read the latest research articles from national and international indexed journal. However, they had lacked basic concepts in the first place and coumpounded by English as languange barrier. This lead to problem of not achieving learning puporses. Thus, there was a need of structured basic concept learning materials of bioremediation. Bioremediation is a process of reducing organic and inorganic pollutants by organisms in the environment. Bioremediation is about real problems, therefore, learning materials of bioremediation will be integrated with Contextual Teaching and Learning (CTL) pedagogical model, to lead students achieve deep comprehension. This was educational Research and Develompment (R&D) using Plomp model which consists of three phases: preliminary research, development or prototyping, and assessment phase. Data gathered as qualitative and quantitave, through interview, questionnaire and paper based test to assess students’ comprehension of bioremediation. Result of this research showed that learning materials of bioremediation were valid from content, layout and presentation, graphics, and linguistic; practical in use for students and lecturer as users; and effective to improve students comprehension of bioremediation.
Students’ Expectations for Blended Learning Discussion in Higher Education
Authors: Rahmi U , Syafril S , Azrul A
Published: June 2021

This study is aimed to describe students’ expectations toward the implementation of blended learning discussions in higher education institutions. This research was conducted to reflect on the ongoing discussion activities so that they can be improved according to student expectations. This investigation was conducted with a qualitative design. Researchers made observations on synchronous discussions and asynchronous discussions, then conducted in-depth interviews with students. Students are given relevant questions related to expectations of discussion in blended learning. The result of the research showed that students have high expectations for the discussion method carried out in blended learning to get more learning opportunities, higher-thinking level practice, collaborate, express opinions, and respect the opinions of others.
Magnetic triggering — time-resolved characterisation of silicon strip modules in the presence of switching DC-DC converters
Authors: Blue A.J. , Gallop B. , Heim T. , Helling C. , Krizka K. , Li B. , Labitan C. , Mladina E. , Poley L. , Phillips P.W. , Santpur S.N. , Sawyer C.A.
Published: June 2021

Modules for the ATLAS Inner Tracker (ITk) strip tracker include a DC-DC converter circuit glued directly to the silicon sensor which converts the 11 V supplied to the module to the 1.5 V required for the operation of the readout chips. The DC-DC converter unit, consisting of a copper solenoid and custom ASIC, is located directly above the silicon strip sensor and therefore needs to be shielded to protect the sensor from EMI noise created during the operation of the circuit. Despite dedicated shielding, consisting of an aluminium shield box with continuous solder seams encompassing the surface components and a copper layer in the PCB beneath it, module channels connected to sensor strips located beneath the converter circuit were found to show a noise increase. While the DC-DC converter unit causing the underlying EMI noise operates at a frequency of 2 MHz, module characterisation measurements for ITk strip tracker modules are typically performed asynchronously to the DC-DC switching and are therefore averaged over the full range of time bins with respect to the converter frequency. In order to investigate the time dependence of the noise injection relative to the DC-DC switching frequency, a dedicated setup to understand the time-resolved performance change in modules was developed. By using a magnetic field probe to measure the field leaking through the shield box and triggering on its rising edge, data taking could be synchronised with the DC-DC switching. This paper illustrates the concept and setup of such time-resolved performance measurements using magnetic triggering and presents results for the observed effects on signal and noise for ATLAS ITk strip modules from both laboratory and beam tests.
Lepton identification performance in jets at a future electron positron Higgs Z factory
Authors: Yu D. , Zheng T. , Ruan M.
Published: June 2021

Identifying the leptons inside jets is critical for the measurements of Higgs boson and the flavor physics program at the CEPC, a proposed Higgs/Z factory with the main ring circumference of 100 km. Using the CEPC baseline software, we analyze the identification performance of leptons generated inside a jet. The jet leptons are identified with typical efficiency and mis-identification rate of 98% and 1% for energy higher than 2 GeV, with the Z → bb process at 91.2 GeV center-of-mass energy. At the benchmark channel of the CEPC flavor program of B

c
→ τν with τ → eνν, the electrons are identified with inclusive efficiency times purity of 97%, providing sufficient signal selection for the physics potential study. Compared to the single leptons, we found that these jet leptons identification efficiency degrades about 1–3%, and the mis-identification rate increases by less than 1% at the same working point. We analyze this effect and found that it is mainly caused by defects in the particle flow reconstruction code in the calorimeters. The dependence between the performance of the shower reconstruction and the lepton identification is quantified.
Global competing water uses for food and energy
Authors: Qin Yue
Published: June 2021

Water competition between the food and energy sector is a critical component of the food-energy-water nexus. However, few studies have systematically characterized the geospatial and, especially, the sub-annual variations in such competition and the associated environmental impacts and targeted mitigation opportunities. This study characterizes competing water uses for crop-specific irrigated agriculture and fuel-specific power generation across global major river basins to reveal their resulting impacts on local water scarcity for global population under both current and a warming climate. Under annual (and most seasonal) accounting, almost all basins currently suffering from extremely high water scarcity are dominated by agricultural water consumption (e.g. accommodating 26%–49% of basin-total population across seasons), which are often simultaneously exposed to potentially decreasing seasonal water availability under a 4 °C warming scenario. Only 13%–20% of population are located in basins dominated by seasonal power sector water uses, which are predominantly with low water scarcity. Agriculture sector provides the most basin-specific water mitigation opportunities across mid-latitude basins in all four seasons. Nevertheless, power sector becomes more important in affecting seasonal water scarcity and provides unique seasonal water mitigation opportunities, particularly in basins among higher northern latitudes in winter. This analysis highlights irrigated agriculture is currently and will likely remain the key in global water management for basins facing the severest water scarcity, yet increasing attention on the seasonal and spatial variations in cross-sector water use competition is needed to better identify region- and season- specific mitigation opportunities.
Assessing the sequestration time scales of some ocean-based carbon dioxide reduction strategies
Authors: Siegel D A , DeVries T , Doney S C , Bell T
Published: June 2021

Ocean-based carbon dioxide (CO2) removal (CDR) strategies are an important part of the portfolio of approaches needed to achieve negative greenhouse gas emissions. Many ocean-based CDR strategies rely on injecting CO2 or organic carbon (that will eventually become CO2) into the ocean interior, or enhancing the ocean’s biological pump. These approaches will not result in permanent sequestration, because ocean currents will eventually return the injected CO2 back to the surface, where it will be brought into equilibrium with the atmosphere. Here, a model of steady state global ocean circulation and mixing is used to assess the time scales over which CO2 injected in the ocean interior remains sequestered from the atmosphere. There will be a distribution of sequestration times for any single discharge location due to the infinite number of pathways connecting a location at depth with the sea surface. The resulting probability distribution is highly skewed with a long tail of very long transit times, making mean sequestration times much longer than typical time scales. Deeper discharge locations will sequester purposefully injected CO2 much longer than shallower ones and median sequestration times are typically decades to centuries, and approach 1000 years in the deep North Pacific. Large differences in sequestration times occur both within and between the major ocean basins, with the Pacific and Indian basins generally having longer sequestration times than the Atlantic and Southern Oceans. Assessments made over a 50 year time horizon illustrates that most of the injected carbon will be retained for injection depths greater than 1000 m, with several geographic exceptions such as the Western North Atlantic. Ocean CDR strategies that increase upper ocean ecosystem productivity with the goal of exporting more carbon to depth will have mainly a short-term influence on atmospheric CO2 levels because ∼70% will be transported back to the surface ocean within 50 years. The results presented here will help plan appropriate ocean CDR strategies that can help limit climate damage caused by fossil fuel CO2 emissions.
Universal break law for a class of models of polymer rupture
Authors: Aurzada Frank , Betz Volker , Lifshits Mikhail
Published: June 2021

We model a polymer by a finite chain of Brownian particles, interacting through a pairwise potentialU. We investigate what happens when one end of the chain is fixed and the other end slowly pulled away, and when we assume that the chain breaks as soon as the distance between two neighbouring particles exceeds a certain thresholdb. We find that under natural conditions onUand suitable scaling of noise and pulling speed, the laws of the break time and of the place along the chain where the break occurs converge to explicit limits. These limits are universal in the sense that they only depend onU″(b).
Two-dimensional binary metal-oxide quasicrystal approximants
Authors: Huran Ahmad W , Wang Hai-Chen , Marques Miguel A L
Published: June 2021

We investigate, using a systematic computational approach, the possibility of the existence of two-dimensional quasicrystalline phases of binary metal-oxides. Our approach relies on the construction of the complete two-dimensional binary phase diagram through the use of unbiased global structural prediction methods. We then identify, in the low-energy periodic phases, structural elements that can be used to generate quasicrystalline phases through an inflation process. In this way we obtain chemically consistent two-dimensional quasicrystal approximants of both barium and titanium oxides. In the proposed structures, the metallic sites occupy the vertices of the aperiodic square-triangle tiling, while the oxygen atoms decorate the interior of the polygons. We then study the properties of the approximants, both free-standing and deposited on a metallic substrate. Finally, we discuss in which circumstances the formation of these phases seems to be favored.
The mean-field limit of quantum Bose gases at positive temperature
Authors: Fröhlich Jürg , Knowles Antti , Schlein Benjamin , Sohinger Vedran
Published: June 2021

We prove that the grand canonical Gibbs state of an interacting quantum Bose gas converges to the Gibbs measure of a nonlinear Schrödinger equation in the mean-field limit, where the density of the gas becomes large and the interaction strength is proportional to the inverse density. Our results hold in dimensions

d
⩽
3

d \leqslant 3

. For

d
>
1

d > 1

the Gibbs measure is supported on distributions of negative regularity and we have to renormalize the interaction. More precisely, we prove the convergence of the relative partition function and of the reduced density matrices in the

L
r

L^r

-norm with optimal exponent

r
r

. Moreover, we prove the convergence in the

L
∞

L^\infty

-norm of Wick-ordered reduced density matrices, which allows us to control correlations of Wick-ordered particle densities as well as the asymptotic distribution of the particle number. Our proof is based on a functional integral representation of the grand canonical Gibbs state, in which convergence to the mean-field limit follows formally from an infinite-dimensional stationary phase argument for ill-defined non-Gaussian measures. We make this argument rigorous by introducing a white-noise-type auxiliary field, through which the functional integral is expressed in terms of propagators of heat equations driven by time-dependent periodic random potentials and can, in turn, be expressed as a gas of interacting Brownian loops and paths. When the gas is confined by an external trapping potential, we control the decay of the reduced density matrices using excursion probabilities of Brownian bridges.
Computing 𝐿-polynomials of Picard curves from Cartier–Manin matrices
Authors: Asif Sualeh , Fité Francesc , Pentland Dylan
Published: June 2021

We study the sequence of zeta functions

Z
(

C
p

,
T
)

Z(C_p,T)

of a generic Picard curve

C
:

y
3

=
f
(
x
)

C:y^3=f(x)

defined over

Q

\mathbb {Q}

at primes

p
p

of good reduction for 

C
C

. We define a degree 9 polynomial

ψ
f

∈

Q

[
x
]

\psi _f\in \mathbb {Q}[x]

such that the splitting field of

ψ
f

(

x
3

/

2
)

\psi _f(x^3/2)

is the

2
2

-torsion field of the Jacobian of

C
C

. We prove that, for all but a density zero subset of primes, the zeta function

Z
(

C
p

,
T
)

Z(C_p,T)

is uniquely determined by the Cartier–Manin matrix

A
p

A_p

of

C
C

modulo

p
p

and the splitting behavior modulo

p
p

of

f
f

and

ψ
f

\psi _f

; we also show that for primes

≡
1

(
mod

3
)

\equiv 1 \pmod {3}

the matrix

A
p

A_p

suffices and that for primes

≡
2

(
mod

3
)

\equiv 2 \pmod {3}

the genericity assumption on

C
C

is unnecessary. An element of the proof, which may be of independent interest, is the determination of the density of the set of primes of ordinary reduction for a generic Picard curve. By combining this with recent work of Sutherland, we obtain a practical deterministic algorithm that computes

Z
(

C
p

,
T
)

Z(C_p,T)

for almost all primes

p
≤
N

p \le N

using

N
log
⁡
(
N

)

3
+
o
(
1
)

N\log (N)^{3+o(1)}

bit operations. This is the first practical result of this type for curves of genus greater than 2.
Non-associative Frobenius algebras for simply laced Chevalley groups
Authors: De Medts Tom , Van Couwenberghe Michiel
Published: June 2021

We provide an explicit construction for a class of commutative, non-associative algebras for each of the simple Chevalley groups of simply laced type. Moreover, we equip these algebras with an associating bilinear form, which turns them into Frobenius algebras. This class includes a 3876-dimensional algebra on which the Chevalley group of typeE8E_8acts by automorphisms. We also prove that these algebras admit the structure of (axial) decomposition algebras.
Fascin-induced actin protrusions are suppressed by dendritic networks in giant unilamellar vesicles
Authors: Wubshet Nadab H. , Bashirzadeh Yashar , Liu Allen P.
Published: June 2021

By reconstituting minimal actin cytoskeletal systems inside giant vesicles, we show that dendritic and bundled actin networks compete to assemble actin networks. Encapsulation of fascin and Arp2/3 complex results in increased dendritic network aggregation and inhibited bundled actin-induced protrusions compared to encapsulating actin and fascin alone.
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry–mass spectrometry
Authors: Lee Joon-Yong , Bilbao Aivett , Conant Christopher R , Bloodsworth Kent J , Orton Daniel J , Zhou Mowei , Wilson Jesse W , Zheng Xueyun , Webb Ian K , Li Ailin , Hixson Kim K , Fjeldsted John C , Ibrahim Yehia M , Payne Samuel H , Jansson Christer , Smith Richard D , Metz Thomas O
Published: June 2021

Motivation

Ion mobility spectrometry (IMS) separations are increasingly used in conjunction with mass spectrometry (MS) for separation and characterization of ionized molecular species. Information obtained from IMS measurements includes the ion’s collision cross section (CCS), which reflects its size and structure and constitutes a descriptor for distinguishing similar species in mixtures that cannot be separated using conventional approaches. Incorporating CCS into MS-based workflows can improve the specificity and confidence of molecular identification. At present, there is no automated, open-source pipeline for determining CCS of analyte ions in both targeted and untargeted fashion, and intensive user-assisted processing with vendor software and manual evaluation is often required.

Results

We present AutoCCS, an open-source software to rapidly determine CCS values from IMS-MS measurements. We conducted various IMS experiments in different formats to demonstrate the flexibility of AutoCCS for automated CCS calculation: (i) stepped-field methods for drift tube-based IMS (DTIMS), (ii) single-field methods for DTIMS (supporting two calibration methods: a standard and a new enhanced method) and (iii) linear calibration for Bruker timsTOF and non-linear calibration methods for traveling wave based-IMS in Waters Synapt and Structures for Lossless Ion Manipulations. We demonstrated that AutoCCS offers an accurate and reproducible determination of CCS for both standard and unknown analyte ions in various IMS-MS platforms, IMS-field methods, ionization modes and collision gases, without requiring manual processing.

Availability and implementation

https://github.com/PNNL-Comp-Mass-Spec/AutoCCS.

Supplementary information

Supplementary data are available at Bioinformatics online. Demo datasets are publicly available at MassIVE (Dataset ID: MSV000085979).
Metabolo-epigenetics: the interplay of metabolism and epigenetics during early germ cells development†
Authors: Verdikt Roxane , Allard Patrick
Published: June 2021

Metabolites control epigenetic mechanisms, and conversly, cell metabolism is regulated at the epigenetic level in response to changes in the cellular environment. In recent years, this metabolo-epigenetic control of gene expression has been implicated in the regulation of multiple stages of embryonic development. The developmental potency of stem cells and their embryonic counterparts is directly determined by metabolic rewiring. Here, we review the current knowledge on the interplay between epigenetics and metabolism in the specific context of early germ cell development. We explore the implications of metabolic rewiring in primordial germ cells in light of their epigenetic remodeling during cell fate determination. Finally, we discuss the relevance of concerted metabolic and epigenetic regulation of primordial germ cells in the context of mammalian transgenerational epigenetic inheritance.
The tailor-made treatment in a particular case of pulmonary hypertension in thalassaemia intermedia: a case report
Authors: Blasi Federico B M , Rota Irene , Graziadei Giovanna , Vicenzi Marco
Published: June 2021

Background

Pulmonary hypertension (PH) is a haemodynamic condition, secondary to different causes. Thalassaemia may lead to PH of different origin and needs a comprehensive analysis to be correctly characterized and possibly treated.

Case summary

We present a case study of a patient with a non-transfusion-dependent thalassaemia and a previous diagnosis of group 5 PH. A complete diagnostic assessment led to a specific diagnosis of chronic thromboembolic PH. Thus, we were able to start a specific therapy with riociguat that provided an improvement in terms of haemodynamic, imaging, and functional status.

Discussion

A correct characterization and treatment of PH are essential in order to change the patient’s prognosis. Chronic thromboembolic PH is a treatable cause of PH in thalassemic patients and should be investigated.
The multiple mediating effects of social connectedness and self-care confidence on the relationship between subjective social status and emotional well-being in patients with heart failure: a cross-sectional study
Authors: Chen Cancan , Zhang Yanting , Zhao Qiuge , Wang Lyu , An Yan , Fan Xiuzhen
Published: June 2021

Background

Previous studies have shown that subjective social status (SSS) was positively associated with well-being in various populations. However, little is known about the relationship considering the underlying mechanism in patients with heart failure (HF).

Aims

The aim was to study the effects of social connectedness and self-care confidence on the relationship between SSS and well-being in patients with HF according to the Reserve Capacity Model.

Methods and results

We recruited 296 patients from a general hospital using convenience sampling. SSS, social connectedness, self-care confidence, and well-being were assessed using self-reported questionnaires. A multiple mediation model was examined using the PROCESS macro in SPSS.

Higher levels of SSS (r = 0.18, P < 0.01), social connectedness (r = 0.21, P < 0.01), and self-care confidence (r = 0.20, P < 0.01) were positively correlated with better emotional well-being, but not with physical well-being. The multiple mediation analysis revealed that the relationship between SSS and emotional well-being was mediated by social connectedness (effect: 0.061, 95% CI [0.014, 0.148]) and self-care confidence (effect: 0.110, 95% CI [0.006, 0.249]) separately, and together in serial (effect: 0.008, 95% CI [0.001, 0.028]).

Conclusions

Social connectedness and self-care confidence are multiple mediators of the relationship between SSS and emotional well-being. Interventions targeting to strengthening social connectedness and self-care confidence may improve emotional well-being directly. In addition, emotional well-being may be improved by enhancing SSS indirectly in patients with HF.
Bacterial colonization of bladder urothelial cells in women with refractory Detrusor Overactivity: the effects of antibiotic therapy
Authors: Ognenovska S , Chen Z , Mukerjee C , Moore K H , Mansfield K J
Published: June 2021

Bacterial infection may have a pathophysiological role in refractory Detrusor Overactivity (DO). The aim of this study was to observe any impact of antibiotic therapy upon bacterial colonization of urothelial cells, and to determine whether a relationship existed between colonization and symptom severity. Mid-stream urine samples were collected as part of a clinical trial of antibiotics in women with refractory DO. Wright stained urothelial cells were categorized according to the degree of bacterial colonization as; ‘clear’ (free of bacteria), or as associated with bacteria that were ‘adjacent’ to the cell or ‘intracellular’ at low or high density. The average percentages were compared with routine microbiology cultures, over the 26 week trial, and with patient clinical outcome measures of DO severity. In patients receiving placebo, ‘high-density intracellular bacteria’ significantly increased during urinary tract infection (P = 0.0008). In antibiotic patients, ‘clear’ cells were more prevalent. Amoxicillin & Clavulanic Acid significantly decreased bacterial colonization within urothelial cells, suggesting that these antibiotics possess the greatest intracellular efficacy. ‘High-density intracellular bacteria’ positively correlated with symptom severity, measured by leakage on pad test (P = 0.014), leaks per day (P = 0.004), and voids per day (P = 0.005). Thus, by decreasing high density intracellular bacteria, antibiotic treatment may improve the refractory DO condition.
A screen for sleep and starvation resistance identifies a wake-promoting role for the auxiliary channel unc79
Authors: Murakami Kazuma , Palermo Justin , Stanhope Bethany A , Gibbs Allen G , Keene Alex C
Published: June 2021

The regulation of sleep and metabolism are highly interconnected, and dysregulation of sleep is linked to metabolic diseases that include obesity, diabetes, and heart disease. Furthermore, both acute and long-term changes in diet potently impact sleep duration and quality. To identify novel factors that modulate interactions between sleep and metabolic state, we performed a genetic screen for their roles in regulating sleep duration, starvation resistance, and starvation-dependent modulation of sleep. This screen identified a number of genes with potential roles in regulating sleep, metabolism, or both processes. One such gene encodes the auxiliary ion channel UNC79, which was implicated in both the regulation of sleep and starvation resistance. Genetic knockdown or mutation of unc79 results in flies with increased sleep duration, as well as increased starvation resistance. Previous findings have shown that unc79 is required in pacemaker for 24-hours circadian rhythms. Here, we find that unc79 functions in the mushroom body, but not pacemaker neurons, to regulate sleep duration and starvation resistance. Together, these findings reveal spatially localized separable functions of unc79 in the regulation of circadian behavior, sleep, and metabolic function.
Smoothened and ARL13B are critical in mouse for superior cerebellar peduncle targeting
Authors: Suciu Sarah K , Long Alyssa B , Caspary Tamara
Published: June 2021

Patients with the ciliopathy Joubert syndrome present with physical anomalies, intellectual disability, and a hindbrain malformation described as the “molar tooth sign” due to its appearance on an MRI. This radiological abnormality results from a combination of hypoplasia of the cerebellar vermis and inappropriate targeting of the white matter tracts of the superior cerebellar peduncles. ARL13B is a cilia-enriched regulatory GTPase established to regulate cell fate, cell proliferation, and axon guidance through vertebrate Hedgehog signaling. In patients, mutations in ARL13B cause Joubert syndrome. To understand the etiology of the molar tooth sign, we used mouse models to investigate the role of ARL13B during cerebellar development. We found that ARL13B regulates superior cerebellar peduncle targeting and these fiber tracts require Hedgehog signaling for proper guidance. However, in mouse, the Joubert-causing R79Q mutation in ARL13B does not disrupt Hedgehog signaling nor does it impact tract targeting. We found a small cerebellar vermis in mice lacking ARL13B function but no cerebellar vermis hypoplasia in mice expressing the Joubert-causing R79Q mutation. In addition, mice expressing a cilia-excluded variant of ARL13B that transduces Hedgehog normally showed normal tract targeting and vermis width. Taken together, our data indicate that ARL13B is critical for the control of cerebellar vermis width as well as superior cerebellar peduncle axon guidance, likely via Hedgehog signaling. Thus, our work highlights the complexity of ARL13B in molar tooth sign etiology.
Elder Mistreatment Methods and Measures in Round 3 of the National Social Life, Health, and Aging Project
Authors: Wong Jaclyn S , Howe Melissa J K , Breslau Hannah , Wroblewski Kristen E , McSorley V Eloesa , Waite Linda J
Published: June 2021

Objectives

Elder mistreatment has negative consequences for older adults’ health and well-being. As such, scholars aim to understand its causes, the contexts in which it occurs, how to prevent victimization, and how to design interventions for mistreated older adults. This paper provides a detailed overview of the 2015–2016 National Social Life, Health, and Aging Project (NSHAP) Round 3 Elder Mistreatment Module (EMM) to encourage further research on the topic.

Method

This paper reviews previous elder mistreatment scholarship, describes the EMM, provides descriptive analyses of elder mistreatment among community-dwelling older adults, and discusses promising approaches and limitations to future research with these data.

Results

The EMM includes 10 stem questions to measure elder mistreatment behaviors experienced since age 60 and 2 follow-up questions about perceived severity and the identity of the perpetrator. The stem questions can be analyzed individually or combined into a scale, and researchers can account for severity as a robustness check. Analysts can also group the measures into specific types of elder mistreatment. A major strength of the EMM is its ability to identify perpetrators in victims’ core social networks.

Discussion

The NSHAP Round 3 EMM provides scholars an opportunity to study older Americans’ mistreatment experiences, particularly as they relate to their physical and mental health, their social networks and personal relationships, and their broader social contexts.
Global Analysis of GG Systems
Authors: Matsubara-Heo Saiei-Jaeyeong
Published: June 2021

This paper deals with some analytic aspects of GG system introduced by I.M. Gelfand and M.I. Graev: we compute the dimension of the solution space of GG system over the field of meromorphic functions periodic with respect to a lattice. We describe the monodromy invariant subspace of the solution space. We provide a connection formula between a pair of bases consisting of $\Gamma $-series solutions of GG system associated with a pair of regular triangulations adjacent to each other in the secondary fan.
Increasing trust in real-world evidence through evaluation of observational data quality
Authors: Blacketer Clair , Defalco Frank J , Ryan Patrick B , Rijnbeek Peter R
Published: June 2021

Objective

Advances in standardization of observational healthcare data have enabled methodological breakthroughs, rapid global collaboration, and generation of real-world evidence to improve patient outcomes. Standardizations in data structure, such as use of common data models, need to be coupled with standardized approaches for data quality assessment. To ensure confidence in real-world evidence generated from the analysis of real-world data, one must first have confidence in the data itself.

Materials and Methods

We describe the implementation of check types across a data quality framework of conformance, completeness, plausibility, with both verification and validation. We illustrate how data quality checks, paired with decision thresholds, can be configured to customize data quality reporting across a range of observational health data sources. We discuss how data quality reporting can become part of the overall real-world evidence generation and dissemination process to promote transparency and build confidence in the resulting output.

Results

The Data Quality Dashboard is an open-source R package that reports potential quality issues in an OMOP CDM instance through the systematic execution and summarization of over 3300 configurable data quality checks.

Discussion

Transparently communicating how well common data model-standardized databases adhere to a set of quality measures adds a crucial piece that is currently missing from observational research.

Conclusion

Assessing and improving the quality of our data will inherently improve the quality of the evidence we generate.
Illustrating potential effects of alternate control populations on real-world evidence-based statistical analyses
Authors: Huang Yidi , Yuan William , Kohane Isaac S , Beaulieu-Jones Brett K
Published: June 2021

Objective

Case–control study designs are commonly used in retrospective analyses of real-world evidence (RWE). Due to the increasingly wide availability of RWE, it can be difficult to determine whether findings are robust or the result of testing multiple hypotheses.

Materials and Methods

We investigate the potential effects of modifying cohort definitions in a case–control association study between depression and type 2 diabetes mellitus. We used a large (>75 million individuals) de-identified administrative claims database to observe the effects of minor changes to the requirements of glucose and hemoglobin A1c tests in the control group.

Results

We found that small permutations to the criteria used to define the control population result in significant shifts in both the demographic structure of the identified cohort as well as the odds ratio of association. These differences remain present when testing against age- and sex-matched controls.

Discussion

Analyses of RWE need to be carefully designed to avoid issues of multiple testing. Minor changes to control cohorts can lead to significantly different results and have the potential to alter even prospective studies through selection bias.

Conclusion

We believe this work offers strong support for the need for robust guidelines, best practices, and regulations around the use of observational RWE for clinical or regulatory decision-making.
Prevalence of a Novel Bunyavirus in Tea Tussock Moth Euproctis pseudoconspersa (Lepidoptera: Lymantriidae)
Authors: Wang Xiaoqing , Gu Qiaoying , Zhang Wei , Jiang Hongyan , Chen Shichun , Smagghe Guy , Niu Jinzhi , Wang Jin-Jun
Published: June 2021

Euproctis pseudoconspersa is a major pest of tea plants, and also causes a skin rash on workers in tea plantations. Research on virus could provide fundamental insights for classification, genetic diversity, evolution, and host–virus interaction mechanisms. Here, we identified a novel RNA virus, Euproctis pseudoconspersa bunyavirus (Phenuiviridae), and found that it is widely distributed in field populations of E. pseudoconspersa. The replication of virus in E. pseudoconspersa was indicated by Tag-PCR. These results contribute to the classification of bunyaviruses and provide insight into the diversity of commensal E. pseudoconspersa bunyavirus and the host.
Toward identification of a putative candidate gene for nutrient mineral accumulation in wheat grains for human nutrition purposes
Authors: Alomari Dalia Z , Alqudah Ahmad M , Pillen Klaus , von Wirén Nicolaus , Röder Marion S
Published: June 2021

A multilocus genome-wide association study of a panel of 369 diverse wheat (Triticum aestivum) genotypes was carried out in order to examine the genetic basis of variations in nutrient mineral concentrations in the grains. The panel was grown under field conditions for three consecutive years and the concentrations of Ca, K, Mg, Mn, P, and S were determined. Wide ranges of natural variation were detected among the genotypes. Strong positive correlations were found among the minerals except for K, which showed negative correlation trends with the other minerals. Genetic association analysis detected 86 significant marker–trait associations (MTAs) underlying the natural variations in mineral concentrations in grains. The major MTA was detected on the long arm of chromosome 5A and showed a pleiotropic effect on Ca, K, Mg, Mn, and S. Further significant MTAs were distributed among the whole genome except for chromosomes 3D and 6D. We identified putative candidate genes that are potentially involved in metal uptake, transport, and assimilation, including TraesCS5A02G542600 on chromosome 5A, which was annotated as a Major Facilitator Superfamily transporter and acted on all the minerals except K. TraesCS5A02G542600 was highly expressed in seed coat, and to a lesser extent in the peduncle, awns, and lemma. Our results provide important insights into the genetic basis of enhancement of nutrient mineral concentrations that can help to inform future breeding studies in order to improve human nutrition.
Pax7 pioneer factor action requires both paired and homeo DNA binding domains
Authors: Pelletier Audrey , Mayran Alexandre , Gouhier Arthur , Omichinski James G , Balsalobre Aurelio , Drouin Jacques
Published: June 2021

The pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 showed that each DBD binds a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed sites for both paired and homeo domains. The present work investigated the implication of the DBDs in pioneer action. We show that the composite sequence is a higher affinity binding site and that efficient binding to this site involves both DBDs of the same Pax7 molecule. This binding is not sensitive to cytosine methylation of the DNA sites consistent with pioneer action within nucleosomal heterochromatin. Introduction of single amino acid mutations in either paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.
Neuroendovascular Management of Acute Ischemic Basilar Strokes: 2-Dimensional Operative Video
Authors: Porto Guilherme B F , Sattur Mithun G , Al Kasab Sami , Spiotta Alejandro M ,   Endovascular Neurosurgery Research Group (ENRG), Arthur Adam , Bain Mark , Bendock Bernard , Jo Binning Mandy , Boulos Alan S , Crowley Webster , Fessler Richard , Grande Andrew , Guterman Lee , Hanel Ricardo , Hoit Daniel , Hopkins L Nelson , Howington Jay , James Robert , Jankowitz Brian , Kan Peter , Khalessi Alex A , Kim Louis , Langer David , Lanzino Giuseppe , Levitt Michael , Levy Elad I , Lopes Demetrius , Mack William , Mericle Robert , Mocco J , Ogilvy Chris , Pandey Aditya , Replogle Robert , Riina Howard , Ringer Andrew , Rodriguez Rafael , Saugaveau Eric , Schirmer Clemens , Siddiqui Adnan H , Spiotta Alex , Sultan Ali , Tawk Rabih , Thomas Ajith , Turner Raymond , Veznedaroglu Erol , Welch Babu , White Jonathan
Published: June 2021

Basilar artery occlusions (BAOs) are devastating ischemic strokes that account for 1% of all strokes with high morbidity and mortality; however, neuroendovascular techniques such as ADAPT have recently revolutionized the clinical outcomes of these patients.
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Common underlying pathology in patients with BAO include intracranial atherosclerotic disease (ICAD) as well as thromboembolic origin.
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Basilar artery ICAD in a setting of acute stroke portends a poor prognosis and post-thrombectomy residual critical flow limiting stenosis treatment options, including balloon angioplasty with or without stent placement.
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We present a video illustration of neuroendovascular technique and challenges encountered when managing this pathology.

Image at 5:42 reprinted with permission from Alawieh et al, Lessons learned over more than 500 stroke thrombectomies using ADAPT with increasing aspiration catheter size, Neurosurgery, 86(1), 2020, pp. 61-70, with permission from the Congress of Neurological Surgeons.
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The Eternal Decline and Fall of Rome
Authors: Watts Edward J.
Published: June 2021

The Eternal Decline and Fall of Rome: The History of a Dangerous Idea traces the development and use of the rhetoric of Roman decline and renewal across 2200 years. Beginning in the Roman Republic at the turn of the second century BC and stretching to the uses of Roman decline in the present day, the book argues that the use of this common rhetoric frequently blamed people for sparking Roman decline. It also evolves over time. In the Republic, politicians like Cato pointed to decline in the present and promised future renewal. Augustus and other emperors beginning a new imperial dynasty often claimed to have sparked a renewal that corrected the decline caused by their predecessors. Early Christian emperors like Constantine and Theodosius I experimented with a rhetoric of progress in which they claimed that Rome’s embrace of Christianity meant it would become better than it ever had been before. The fifth-century loss of the West forced Christians like Augustine to disentangle Christian and Roman progress. It also enabled the Eastern emperor Justinian to justify invasions of Africa, Italy, and Spain as restorations of lost territories to Roman rule. Western emperors ranging from Charlemagne to Charles V used similar claims to support military action directed from the West against the East. Figures as diverse as Napoleon and Mussolini show that the allure of restoring Rome remained potent into the twentieth century, but the story of Rome’s decline and fall, popularized by eighteenth-century writers like Montesquieu and Gibbon, is now most frequently evoked as a warning about the consequence of social or political change.
The Republic of Violence and the Empire of Peace
Authors: Watts Edward J.
Published: June 2021

Both conservatives in the senate and populist reformers learned how to use violence as a political tool in the years after Tiberius Gracchus’s murder. Populists allied with figures like Marius made increasingly effective use of mobs to sway elections. The senate used the senatus consultum ultimum to deprive citizens of their rights. Sulla’s use of his army to seize power over Rome and dictate the terms of his restoration of the Republic represented a natural evolution of this process. By the late 50s BC, it had again become clear that Republican political norms had deteriorated to such a degree that prominent citizens could not trust that their rights would be protected. In Cicero’s formulation, Rome had become a Republic of violence. This violent climate prompted Julius Caesar’s march on Rome, but it took Augustus’s victory in the civil war with Antony to fully restore peace and the rule of law.
Renewal without Decline: The Antonines and Severans
Authors: Watts Edward J.
Published: June 2021

The political stability of the Antonine dynasty saw emperors and the authors describing their reigns both move away from claims that problems in the empire had been caused by imperial predecessors. What emerged instead under the emperor Hadrian was a focus on restorations of the empire without blaming previous emperors for causing Rome to decline, a way of describing change that Antoninus Pius and Marcus Aurelius followed. The Severan dynasty did as well, especially after Septimius Severus manufactured connections to his Antonine imperial predecessors in order to create the illusion of political continuity. This illusion of prosperous continuity gives the misleading impression of a thriving empire. Instead, for much of the later second century, Romans suffered from maladies as diverse as barbarian invasions and the deadly Antonine Plague. As conditions deteriorated under Alexander Severus, however, authors like Cassius Dio and, later, Herodian again return to the old way of speaking about Roman decline.
Introduction: The Reformed Conformist Style of Piety
Authors: Hampton Stephen
Published: June 2021

This Introduction opens with an account of the consecration of Exeter College Chapel in 1624 and explains why the ceremony cannot accurately be described as either ‘Laudian’ or ‘Puritan,’ since it reflects theological emphases associated with both groups. It goes on to establish that the historiography of the Early Stuart period has generally acknowledged the presence of English clergy who were committed to both an orthodox Reformed understanding of grace and the established polity of the Church, although no dedicated analysis of their religious tradition has been undertaken before the present study. The ten significant Reformed Conformist theologians who will be the focus of the study are then introduced, and the personal links between them set out.
Responses to Montagu
Authors: Hampton Stephen
Published: June 2021

Chapter 3 discusses the immediate responses to Montagu’s work undertaken by a number of Reformed Conformists. It exhibits the range of polemical approaches they used and establishes that Reformed Conformists were in the vanguard of the public opposition to Montagu. Featley’s Parallels illustrate how Reformed Conformists brought the teaching of the academy to bear within the public sphere. His Ancilla exhibits the use of devotional literature to advance their cause. Ward’s Gratia Discriminans sets out the Reformed Conformist case that their theology of grace did not undermine human free choice. Carleton’s Examination addressed Montagu’s suggestion that a Reformed view of grace was a manifestation of Puritanism and asserted its consonance with the Thirty-nine Articles. Hall’s unpublished Via Media, by contrast, advocated an irenic and moderate reading of English orthodoxy, but one in which there was still no room for any teaching that made salvation ultimately dependent on the human will.