bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample size calculation for cluster randomized trials with zero‐inflated count outcomes
Authors: Zhou Zhengyang , Li Dateng , Zhang Song 
Published: February 2022

AbstractCluster randomized trials (CRT) have been widely employed in medical and public health research. Many clinical count outcomes, such as the number of falls in nursing homes, exhibit excessive zero values. In the presence of zero inflation, traditional power analysis methods for count data based on Poisson or negative binomial distribution may be inadequate. In this study, we present a sample size method for CRTs with zero‐inflated count outcomes. It is developed based on GEE regression directly modeling the marginal mean of a zero‐inflated Poisson outcome, which avoids the challenge of testing two intervention effects under traditional modeling approaches. A closed‐form sample size formula is derived which properly accounts for zero inflation, ICCs due to clustering, unbalanced randomization, and variability in cluster size. Robust approaches, including t‐distribution‐based approximation and Jackknife re‐sampling variance estimator, are employed to enhance trial properties under small sample sizes. Extensive simulations are conducted to evaluate the performance of the proposed method. An application example is presented in a real clinical trial setting.
Unraveling the Kinematics of Sperm Motion by Reconstructing the Flagellar Wave Motion in 3D
Authors: Powar Sushant , Parast Farin Yazdan , Nandagiri Ashwin , Gaikwad Avinash S. , Potter David L. , O'Bryan Moira K. , Prabhakar Ranganathan , Soria Julio , Nosrati Reza 
Published: February 2022

AbstractSperm swim through the female reproductive tract by propagating a 3D flagellar wave that is self‐regulatory in nature and driven by dynein motors. Traditional microscopy methods fail to capture the full dynamics of sperm flagellar activity as they only image and analyze sperm motility in 2D. Here, an automated platform to analyze sperm swimming behavior in 3D by using thin‐lens approximation and high‐speed dark field microscopy to reconstruct the flagellar waveform in 3D is presented. It is found that head‐tethered mouse sperm exhibit a rolling beating behavior in 3D with the beating frequency of 6.2 Hz using spectral analysis. The flagellar waveform bends in 3D, particularly in the distal regions, but is only weakly nonplanar and ambidextrous in nature, with the local helicity along the flagellum fluctuating between clockwise and counterclockwise handedness. These findings suggest a nonpersistent flagellar helicity. This method provides new opportunities for the accurate measurement of the full motion of eukaryotic flagella and cilia which is essential for a biophysical understanding of their activation by dynein motors.
Does astrocyte gap junction protein expression differ during development in absence epileptic rats?
Authors: Köse Büşra , Özkan Mazhar , Sur‐Erdem İlknur , Çavdar Safiye 
Published: February 2022

AbstractIntercellular communication via gap junctions (GJs) has a wide variety of complex and essential functions in the CNS. In the present developmental study, we aimed to quantify the number of astrocytic GJs protein connexin 30 (Cx30) of genetic model of absence epilepsy rats from Strasbourg (GAERS) at postnatal P10, P30, and P60 days in the epileptic focal areas involved in the cortico‐thalamic circuit. We compared the results with Wistar rats using immunohistochemistry and western blotting. The number of Cx30 immunopositive astrocytes per unit area were quantified for the somatosensory cortex (SSCx), ventrobasal (VB), and lateral geniculate (LGN) thalamic nuclei of the two strains and Cx30 western blot was applied to the tissue samples from the same regions. Both immunohistochemical and western blot results revealed the presence of Cx30 in all regions studied at P10 in both Wistar and GAERS animals. The SSCx, VB, and LGN of Wistar animals showed progressive increase in the number of Cx30 immunopositive labeled astrocytes from P10 to P30 and reached a peak at P30; then a significant decline was observed from P30 to P60 for the SSCx and VB. However, in GAERS Cx30 immunopositive labeled astrocytes showed a progressive increase from P10 to P60 for all brain regions studied. The immunohistochemical data highly corresponded with western blotting results. We conclude that the developmental disproportional expression of Cx30 in the epileptic focal areas in GAERS may be related to the onset of absence seizures or may be related to the neurogenesis of absence epilepsy.
Effect of aspect ratio subjected to wind hazard in tall buildings situated along the coastal line of India
Authors: Ghosh Tamal , Sil Arjun 
Published: February 2022

SummaryThe escalating growth of the tall buildings as well as the increasing number of extreme wind events in the Indian coastal region have certainly arisen the question of the safety and stability of these buildings situated in the metropolitan cities along the coastline. In such a scenario where there have been a constant focus on more researches for a unified wind code, however a comprehensive comparative study is required not only to assess and analyze the dynamic peak factors of the tall building models due to wind load, but also to enlighten the differences in the obtained results as well as their patterns respectively. The aspect ratio of buildings essentially governs the stability as well as contributes to a great extent on the dynamic responses in terms of base shear, base moment and torsional effects at the base. However, a framework based on the Indian wind database could ease the complexity of such parametric survivability studies of such structures. Distinguished variations in the dynamic responses for a series of models of tall buildings with varying aspect ratios along the height are analyzed as well as discussed in the present study, and the pattern of the deviation of the results with a parallel framework is also addressed to propose a mechanism for assessing the behaviors of tall buildings under specific wind speed predominant in the Indian coastal region that would help to ensure the safety and stability of structures subjected to wind hazards in Indian context in future.
A case of generalised cutaneous apocrine cystomatosis in a Pekingese dog
Authors: Stazi Marica , Silvestri Serenella , Mechelli Luca , Brachelente Chiara 
Published: February 2022

AbstractClinical, histological and immunohistochemical examination of a 13‐year‐old male client‐owned Pekingese dog revealed an uncommon presentation of apocrine cutaneous cystomatosis. This is a rare non‐neoplastic condition of uncertain cause, characterised by multiple cystically dilated apocrine sweat glands. We aimed to describe the features of this unusual case of generalised cutaneous apocrine cystomatosis in the dog, which can be useful to distinguish it from multifocal benign cystic apocrine tumours.
Circadian rhythms of the mRNA abundances of clock genes and glucose transporters in the jejunum of weanling‐growing pigs
Authors: Kinoshita Yuki , Takahashi Hayata , Katsumata Masaya 
Published: February 2022

AbstractBackgroundWhether abundance of glucose transporter mRNAs in the small intestine of pigs shows circadian rhythms and its regulation by clock genes was still unknown.ObjectivesWe examined whether the abundance of glucose transporters and clock genes mRNAs in the small intestine of pigs shows circadian rhythms.MethodsTwenty barrows (4 weeks old) were reared under 12 h bright and 12 h dark lighting conditions. During the 3‐week feeding trial, pigs were allowed free access to feed. The abundances of the mRNA of glucose transporters (SGLT1 and GLUT2) and clock genes (Bmal1, Per1, Per2, and Cry2) in the intestine were measured at four time points (ZT2, ZT8, ZT14, and ZT20).ResultsIn the jejunum, the abundance of SGLT1 mRNA was higher at ZT20 and ZT2 and lower at ZT8 and ZT14 (p < 0.05). The abundances of GLUT2 mRNA in the jejunum at ZTs 20 and 2 were tended to be higher than those at ZTs 8 and 14 (p = 0.05). In the jejunum, the abundance of Bmal1 mRNA was higher at ZT8 and ZT14 than at ZT20 and ZT2 (p < 0.05). Further, the abundance of Per1 mRNA at ZT2 was higher than those at the other sampling times (p < 0.05). The abundance of Per1 mRNA at ZT8 was higher than that at ZT14 (p < 0.05), while that of Per2 mRNA was higher at ZT2 than those at ZTs 20 and 14 (p < 0.05).ConclusionWe speculate that these circadian rhythms of abundances of glucose transporter mRNAs are regulated by the clock genes expressed in the jejunum.
Loomis–Whitney inequalities in Heisenberg groups
Authors: Fässler Katrin , Pinamonti Andrea 
Published: February 2022

AbstractThis note concernsLoomis–Whitney inequalitiesin Heisenberg groups$$\mathbb {H}^n$$Hn:$$\begin{aligned} |K| \lesssim \prod _{j=1}^{2n}|\pi _j(K)|^{\frac{n+1}{n(2n+1)}}, \qquad K \subset \mathbb {H}^n. \end{aligned}$$|K|≲∏j=12n|πj(K)|n+1n(2n+1),K⊂Hn.Here$$\pi _{j}$$πj,$$j=1,\ldots ,2n$$j=1,…,2n, are thevertical Heisenberg projectionsto the hyperplanes$$\{x_j=0\}$${xj=0}, respectively, and$$|\cdot |$$|·|refers to a natural Haar measure on either$$\mathbb {H}^n$$Hn, or one of the hyperplanes. The Loomis–Whitney inequality in the first Heisenberg group$$\mathbb {H}^1$$H1is a direct consequence of known$$L^p$$Lpimproving properties of the standard Radon transform in$$\mathbb {R}^2$$R2. In this note, we show how the Loomis–Whitney inequalities in higher dimensional Heisenberg groups can be deduced by an elementary inductive argument from the inequality in$$\mathbb {H}^1$$H1. The same approach, combined with multilinear interpolation, also yields the following strong type bound:$$\begin{aligned} \int _{\mathbb {H}^n} \prod _{j=1}^{2n} f_j(\pi _j(p))\;dp\lesssim \prod _{j=1}^{2n} \Vert f_j\Vert _{\frac{n(2n+1)}{n+1}} \end{aligned}$$∫Hn∏j=12nfj(πj(p))dp≲∏j=12n‖fj‖n(2n+1)n+1for all nonnegative measurable functions$$f_1,\ldots ,f_{2n}$$f1,…,f2non$$\mathbb {R}^{2n}$$R2n. These inequalities and their geometric corollaries are thus ultimately based on planar geometry. Among the applications of Loomis–Whitney inequalities in$$\mathbb {H}^n$$Hn, we mention the following sharper version of the classical geometric Sobolev inequality in$$\mathbb {H}^n$$Hn:$$\begin{aligned} \Vert u\Vert _{\frac{2n+2}{2n+1}} \lesssim \prod _{j=1}^{2n}\Vert X_ju\Vert ^{\frac{1}{2n}}, \qquad u \in BV(\mathbb {H}^n), \end{aligned}$$‖u‖2n+22n+1≲∏j=12n‖Xju‖12n,u∈BV(Hn),where$$X_j$$Xj,$$j=1,\ldots ,2n$$j=1,…,2n, are the standard horizontal vector fields in$$\mathbb {H}^n$$Hn. Finally, we also establish an extension of the Loomis–Whitney inequality in$$\mathbb {H}^n$$Hn, where the Heisenberg vertical coordinate projections$$\pi _1,\ldots ,\pi _{2n}$$π1,…,π2nare replaced by more general families of mappings that allow us to apply the same inductive approach based on the$$L^{3/2}$$L3/2-$$L^3$$L3boundedness of an operator in the plane.
Systematic identification of trimethoprim metabolites in lettuce
Authors: Tadić Đorđe , Gramblicka Michal , Mistrik Robert , Bayona Josep Maria 
Published: February 2022

AbstractAntibiotics are some of the most widely used drugs. Their release in the environment is of great concern since their consumption is a major factor for antibiotic resistance, one of the most important threats to human health. Their occurrence and fate in agricultural systems have been extensively investigated in recent years. Yet whilst their biotic and abiotic degradation pathways have been thoroughly researched, their biotransformation pathways in plants are less understood, such as in case of trimethoprim. Although trimethoprim has been reported in the environment, its fate in higher plants still remains unknown. A bench-scale experiment was performed and 30 trimethoprim metabolites were identified in lettuce (Lactuca sativa L.), of which 5 belong to phase I and 25 to phase II. Data mining yielded a list of 1018 ions as possible metabolite candidates, which was filtered to a final list of 87 candidates. Molecular structures were assigned for 19 compounds, including 14 TMP metabolites reported for the first time. Alongside well-known biotransformation pathways in plants, additional novel pathways were suggested, namely, conjugation with sesquiterpene lactones, and abscisic acid as a part of phase II of plant metabolism. The results obtained offer insight into the variety of phase II conjugates and may serve as a guideline for studying the metabolization of other chemicals that share a similar molecular structure or functional groups with trimethoprim. Finally, the toxicity and potential contribution of the identified metabolites to the selective pressure on antibiotic resistance genes and bacterial communities via residual antimicrobial activity were evaluated.
Dynamic service area sizing in urban delivery
Authors: Ulmer Marlin W. , Erera Alan , Savelsbergh Martin 
Published: February 2022

AbstractWe consider an urban instant delivery environment, e.g., meal delivery, in which customers place orders over the course of a day and are promised delivery within a short period of time after an order is placed. Deliveries are made using a fleet of vehicles, each completing one or more trips during the day. To avoid missing delivery time promises as much as possible, the provider manages demand by dynamically adjusting the size of the service area, i.e., the area in which orders can be delivered. The provider seeks to maximize the number of orders served while avoiding missed delivery time promises. We present three techniques to support the dynamic adjusting of the size of the service area which can be embedded in planning and execution tools that help the provider achieve its goal. First, we learn the functional dependency between expected demand and the service area that can be supported with the fleet of vehicles. Second, we use value function approximation to improve an initial service area sizing plan for the day based on expected demand. Finally, we introduce a correction mechanism to dynamically adjust the service area sizing plan in response to observed realized demand. Extensive computational experiments demonstrate the efficacy of the techniques and show that dynamic sizing of the service area can increase the number of orders served significantly without increasing the number of missed delivery time promises.
Impact of type of minimally invasive approach on open conversions across ten common procedures in different specialties
Authors: Shah Paresh C. , de Groot Alexander , Cerfolio Robert , Huang William C. , Huang Kathy , Song Chao , Li Yanli , Kreaden Usha , Oh Daniel S. 
Published: February 2022

Abstract
Background
Conversion rates during minimally invasive surgery are generally examined in the limited scope of a particular procedure. However, for a hospital or payor, the cumulative impact of conversions during commonly performed procedures could have a much larger negative effect than what is appreciated by individual surgeons. The aim of this study is to assess open conversion rates during minimally invasive surgery (MIS) across common procedures using laparoscopic/thoracoscopic (LAP/VATS) and robotic-assisted (RAS) approaches.

Study design
Retrospective cohort study using the Premier Database on patients who underwent common operations (hysterectomy, lobectomy, right colectomy, benign sigmoidectomy, low anterior resection, inguinal and ventral hernia repair, and partial nephrectomy) between January 2013 and September 2015. ICD-9 and CPT codes were used to define procedures, modality, and conversion. Propensity scores were calculated using patient, hospital, and surgeon characteristics. Propensity-score matched analysis was used to compare conversions between LAP/VATS and RAS for each procedure.

Results
A total of 278,520 patients had MIS approaches of the ten operations. Conversion occurred in 5% of patients and was associated with a 1.77 day incremental increase in length of stay and $3441 incremental increase in cost. RAS was associated with a 58.5% lower rate of conversion to open surgery compared to LAP/VATS.

Conclusion
At a health system or payer level, conversion to open is detrimental not just for the patient and surgeon but also puts a significant strain on hospital resources. Use of RAS was associated with less than half of the conversion rate observed for LAP/VATS.
Causality in requirements artifacts: prevalence, detection, and impact
Authors: Frattini Julian , Fischbach Jannik , Mendez Daniel , Unterkalmsteiner Michael , Vogelsang Andreas , Wnuk Krzysztof 
Published: February 2022

AbstractCausal relations in natural language (NL) requirements convey strong, semantic information. Automatically extracting such causal information enables multiple use cases, such as test case generation, but it also requires to reliably detect causal relations in the first place. Currently, this is still a cumbersome task as causality in NL requirements is still barely understood and, thus, barely detectable. In our empirically informed research, we aim at better understanding the notion of causality and supporting the automatic extraction of causal relations in NL requirements. In a first case study, we investigate 14.983 sentences from 53 requirements documents to understand the extent and form in which causality occurs. Second, we present and evaluate a tool-supported approach, called CiRA, for causality detection. We conclude with a second case study where we demonstrate the applicability of our tool and investigate the impact of causality on NL requirements. The first case study shows that causality constitutes around 28 % of all NL requirements sentences. We then demonstrate that our detection tool achieves a macro-$$\hbox {F}_{1}$$F1score of 82 % on real-world data and that it outperforms related approaches with an average gain of 11.06 % in macro-Recall and 11.43 % in macro-Precision. Finally, our second case study corroborates the positive correlations of causality with features of NL requirements. The results strengthen our confidence in the eligibility of causal relations for downstream reuse, while our tool and publicly available data constitute a first step in the ongoing endeavors of utilizing causality in RE and beyond.
Anion-type modulates the effect of salt stress on saline lake bacteria
Authors: Csitári Bianka , Bedics Anna , Felföldi Tamás , Boros Emil , Nagy Hajnalka , Máthé István , Székely Anna J. 
Published: February 2022

AbstractBeside sodium chloride, inland saline aquatic systems often contain other anions than chloride such as hydrogen carbonate and sulfate. Our understanding of the biological effects of salt composition diversity is limited; therefore, the aim of this study was to examine the effect of different anions on the growth of halophilic bacteria. Accordingly, the salt composition and concentration preference of 172 strains isolated from saline and soda lakes that differed in ionic composition was tested using media containing either carbonate, chloride or sulfate as anion in concentration values ranging from 0 to 0.40 mol/L. Differences in salt-type preference among bacterial strains were observed in relationship to the salt composition of the natural habitat they were isolated from indicating specific salt-type adaptation. Sodium carbonate represented the strongest selective force, while majority of strains was well-adapted to growth even at high concentrations of sodium sulfate. Salt preference was to some extent associated with taxonomy, although variations even within the same bacterial species were also identified. Our results suggest that the extent of the effect of dissolved salts in saline lakes is not limited to their concentration but the type of anion also substantially impacts the growth and survival of individual microorganisms.
Preliminary MRI-based investigation of characteristics and prognosis of knee bone marrow edema in children with juvenile idiopathic arthritis
Authors: Yang Yang , Yuan Xinyu , Wang Xinning , Tao Ran , Jiang Tao 
Published: February 2022

Abstract

Introduction
Bone marrow edema (BME) is one of the main imaging characteristics of juvenile idiopathic arthritis (JIA) in children and rheumatoid arthritis (RA) in adult. Previous studies have shown that BME occurred in approximately 64% of adults with RA and was a key predictor of poor prognosis. But BME with JIA has not been of great concern. Therefore, we evaluated the prevalence, characteristics, and prognosis of knee joint BME in children with JIA.

Methods
In this retrospective study, we included children with JIA and knee joint involvement from January 2017 to December 2019. BME was evaluated according to the Juvenile Arthritis MRI Scoring system. Clinical characteristics were compared between the BME group and the non-BME group. The characteristics and prognosis of the BME were observed.

Results
A total of 128 children with 136 knee joint MRI data were identified, with 37 knee joints (27.2%) having BME. BME has positive correlation with synovial hypertrophy (Rs = 0.562, p = 0.019). There were significant differences in age (p = 0.010) and disease duration (p = 0.013) between the BME and non-BME groups. BME was found to be more common in older children and the patients with long duration of disease. Locations with BME were the lateral tibial plateau (17/37, 45.9%), the lateral weight-bearing femur (16/37, 43.2%), the medial tibial plateau and the medial femoral condyle (both with 15/37, 40.5%), and the medial weight-bearing femur (12/37, 32.4%). The lateral femoral condyle and both the lateral and medial sides of the patella were rarely involved. Of the 15 BME joints with the MRI follow-up data (interval 6.5 ± 3.0 months), the lesions disappeared or improved within 12 months after the treatments in 13 (86.7%) joints.

Conclusions
The prevalence of knee BME in JIA was 27.2%. There was positive correlation between BME and synovial hypertrophy. Older children and children with long disease duration had a higher risk for BME, which was commonly a late presentation and more likely involved the weight-bearing surfaces of the joint. The overall prognosis was satisfactory after the standard treatments.

Key Points• To the best of our knowledge, this paper is the first one to investigate the MRI manifestation in JIA focus on knee BME sign.
Generation of chimeric kidneys using progenitor cell replacement: Oshima Award Address 2021
Authors: Yamanaka Shuichiro 
Published: February 2022

AbstractIt is believed that the development of new renal replacement therapy (RRT) will increase treatment options for end-stage kidney disease and help reduce the mismatch between supply and demand. Technological advancement in the development of kidney organoids derived from pluripotent stem cells and xenotransplantation using porcine kidneys has been accelerated by a convergence of technological innovations, including the discovery of induced pluripotent stem cells and genome editing, and improvement of analysis techniques such as single-cell ribonucleic acid sequencing. Given the difficulty associated with kidney regeneration, hybrid kidneys are studied as an innovative approach that involves the use of stem cells to generate kidneys, with animal fetal kidneys used as a scaffold. Hybrid kidney technology entails the application of local chimerism for the generation of chimeric kidneys from exogenous renal progenitor cells by borrowing complex nephrogenesis programs from the developmental environment of heterologous animals. Hybrid kidneys can also utilize the urinary tract and bladder tissue of animal fetuses for urine excretion. Generating nephrons from syngeneic stem cells to increase self-cell ratio in xeno-tissues can reduce the risk of xeno-rejection. We showed that nephrons can be generated by ablation of host nephron progenitor cells (NPCs) in the nephron development region of animals and replacing them with exogenous NPCs. This progenitor cell replacement is the basis of hybrid kidney regeneration from progenitor cells using chimera technology. The goal of xeno-regenerative medicine using hybrid kidneys is to overcome serious organ shortage.