bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and control of a running spring-mass model with a trunk based on virtual pendulum concept
Authors: Karagoz O K , Secer G , Ankarali M M , Saranli U 
Published: May 2022

Abstract
The spring-loaded inverted pendulum model has been one of the most studied conceptual models in the locomotion community. Even though it can adequately explain the center of mass trajectories of numerous legged animals, it remains insufficient in template-based control of complex robot platforms, being unable to capture additional dynamic characteristics of locomotion exhibited in additional degrees of freedom such as trunk pitch oscillations. In fact, analysis of trunk behavior during locomotion has been one of the motivations behind studying the virtual pivot point (VPP) concept, with biological inspiration and basis for both natural and synthetic systems with non-negligible trunk dynamics. This study first presents a comprehensive analysis of the VPP concept for planar running behaviors, followed by a systematic study of the existence and characteristics of periodic solutions. In particular, we investigate how periodic solutions depend on model control parameters and compare them based on stability and energetic cost. We then develop a feedback controller that can stabilize system dynamics around its periodic solutions and evaluate performance as compared to a previously introduced controller from the literature. We demonstrate the effectiveness of both controllers and find that the proposed control scheme creates larger basins of attraction with minor degradation in convergence speed. In conclusion, this study shows that the VPP concept, in conjunction with the proposed controller, could be beneficial in designing and controlling legged robots capable of running with non-trivial upper body dynamics. Our systematic analysis of periodic solutions arising from the use of the VPP concept is also an important step towards a more formal basis for comparisons of the VPP concept with bio-locomotion.
BayeshERG: a robust, reliable and interpretable deep learning model for predicting hERG channel blockers
Authors: Kim Hyunho , Park Minsu , Lee Ingoo , Nam Hojung 
Published: May 2022

Abstract
Unintended inhibition of the human ether-à-go-go-related gene (hERG) ion channel by small molecules leads to severe cardiotoxicity. Thus, hERG channel blockage is a significant concern in the development of new drugs. Several computational models have been developed to predict hERG channel blockage, including deep learning models; however, they lack robustness, reliability and interpretability. Here, we developed a graph-based Bayesian deep learning model for hERG channel blocker prediction, named BayeshERG, which has robust predictive power, high reliability and high resolution of interpretability. First, we applied transfer learning with 300 000 large data in initial pre-training to increase the predictive performance. Second, we implemented a Bayesian neural network with Monte Carlo dropout to calibrate the uncertainty of the prediction. Third, we utilized global multihead attentive pooling to augment the high resolution of structural interpretability for the hERG channel blockers and nonblockers. We conducted both internal and external validations for stringent evaluation; in particular, we benchmarked most of the publicly available hERG channel blocker prediction models. We showed that our proposed model outperformed predictive performance and uncertainty calibration performance. Furthermore, we found that our model learned to focus on the essential substructures of hERG channel blockers via an attention mechanism. Finally, we validated the prediction results of our model by conducting in vitro experiments and confirmed its high validity. In summary, BayeshERG could serve as a versatile tool for discovering hERG channel blockers and helping maximize the possibility of successful drug discovery. The data and source code are available at our GitHub repository (https://github.com/GIST-CSBL/BayeshERG).
Improving the nutritional value and bioactivity of soybean meal in solid-state fermentation using Bacillus strains newly isolated from the gut of the termite Termes propinquus
Authors: Nualkul Maneeploy , Yuangsoi Bundit , Hongoh Yuichi , Yamada Akinori , Deevong Pinsurang 
Published: May 2022

Abstract
The present study aimed to isolate and characterize proteolytic Bacillus spp. from termite guts to test the possibility of application for improving the nutritional value and bioactivity of fermented soybean meal (FSBM). Aerobic endospore-forming bacteria were isolated from the gut of the termite Termes propinquus. Ten isolates with high levels of soy milk degradation were selected and tested for extracellular enzyme production. Among them, two isolates, Tp-5 and Tp-7, exhibited all tested hydrolytic enzyme activities (cellulase, xylanase, pectinase, amylase, protease, lipase and phytase), weak alpha hemolytic and also antagonistic activities against fish pathogenic species of Aeromonas and Streptococcus. Both phylogenetic and biochemical analyses indicated that they were closely related to Bacillus amyloliquefaciens. During solid-state fermentation of SBM, Tp-5 and Tp-7 exhibited the highest protease activity (1127.2 and 1552.4 U g–1, respectively) at 36 h, and the resulting FSBMs showed a significant increase in crude protein content and free radical-scavenging ability (P &lt; 0.05), as well as an improvement in the composition of amino acids, metabolites and other nutrients, while indigestible materials such as fiber, lignin and hemicellulose were decreased. The potential strains, especially Tp-7, improved the nutritional value of FSBM by their strong hydrolytic and antioxidant activities, together with reducing antinutritional components.
Long-Term Outcomes of the Excluded Rectum in Crohn’s Disease: A Multicenter International Study
Authors: Kassim Gassan , Yzet Clara , Nair Nilendra , Debebe Anketse , Rendon Alexa , Colombel Jean-Frédéric , Traboulsi Cindy , Rubin David T , Maroli Annalisa , Coppola Elisabetta , Carvello Michele M , Ben David Nadat , De Lucia Francesca , Sacchi Matteo , Danese Silvio , Spinelli Antonino , Hirdes Meike M C , ten Hove Joren , Oldenburg Bas , Cholapranee Aurada , Riter Maxine , Lukin Dana , Scherl Ellen , Eren Esen , Sultan Keith S , Axelrad Jordan , Sachar David B 
Published: May 2022

Abstract

Background
Many patients with Crohn’s disease (CD) require fecal diversion. To understand the long-term outcomes, we performed a multicenter review of the experience with retained excluded rectums.

Methods
We reviewed the medical records of all CD patients between 1990 and 2014 who had undergone diversionary surgery with retention of the excluded rectum for at least 6 months and who had at least 2 years of postoperative follow-up.

Results
From all the CD patients in the institutions’ databases, there were 197 who met all our inclusion criteria. A total of 92 (46.7%) of 197 patients ultimately underwent subsequent proctectomy, while 105 (53.3%) still had retained rectums at time of last follow-up. Among these 105 patients with retained rectums, 50 (47.6%) underwent reanastomosis, while the other 55 (52.4%) retained excluded rectums. Of these 55 patients whose rectums remained excluded, 20 (36.4%) were symptom-free, but the other 35 (63.6%) were symptomatic. Among the 50 patients who had been reconnected, 28 (56%) were symptom-free, while 22(44%) were symptomatic. From our entire cohort of 197 cases, 149 (75.6%) either ultimately lost their rectums or remained symptomatic with retained rectums, while only 28 (14.2%) of 197, and only 4 (5.9%) of 66 with initial perianal disease, were able to achieve reanastomosis without further problems. Four patients developed anorectal dysplasia or cancer.

Conclusions
In this multicenter cohort of patients with CD who had fecal diversion, fewer than 15%, and only 6% with perianal disease, achieved reanastomosis without experiencing disease persistence.
Similar forms have similar functions: dental microwear variability in Tasmanian devils
Authors: Reside Anna , Desantis Larisa R G 
Published: May 2022

Abstract
Dental microwear texture analysis (DMTA) is commonly used to assess the dietary ecology of modern and fossil taxa. In carnivorans, teeth with different functions record dietary behavior differently. Here, we assess DMTA variability along the tooth row of an extant carnivorous marsupial—the Tasmanian devil, Sarcophilus harrisii—which has multiple carnassial-like molars that may function and record diet similarly. We compared the complexity (Asfc), anisotropy (epLsar), and textural fill volume (Tfv) of the lower second, third, and fourth molars of Tasmanian devils to test the hypothesis that teeth with similar forms yield similar functions. Although third molars do have significantly higher epLsar values than fourth molars, all other DMTA attributes are indistinguishable from one another. These data suggest that teeth with comparable morphologies in the same taxon have similar functions and largely record diet similarly. In addition, we compared fossil and modern specimens of S. harrisii from Tasmania to assess dietary behavior over time. These analyses indicate that foods with similar textures have been consumed since the late Quaternary.
A Critique and Refinement of the Wakefieldian Concept of Disorder: An Improvement of the Harmful Dysfunction Analysis
Authors: Smith Emmanuel 
Published: May 2022

Abstract
One way in which bioethicists can benefit the medical community is by clarifying the concept of disorder. Since insurance companies refer to the DSM for whether a patient should receive assistance, one must consider the consequences of one’s concept of disorder for who should be provided with care. I offer a refinement of Jerome Wakefield’s hybrid concept of disorder, the harmful dysfunction analysis. I criticize both the factual component and the value component of Wakefield’s account and suggest how they might be improved. I propose that the factual component should be statistical variation analyzed in multilevel and chronological compilations of physiological data. I propose that the value component should prioritize the individual’s authority regarding the experience of suffering from a physiological condition. My account preserves the insight of using a factual and a value component while avoiding the problems that Wakefield’s original account faces.
Density exponent analysis: gravity-driven steepening of the density profiles of star-forming regions
Authors: Li Guang-Xing , Zhou Ji-Xuan 
Published: May 2022

ABSTRACTThe evolution of molecular interstellar clouds is a complex, multiscale process. The power-law density exponent describes the steepness of density profiles, and it has been used to characterize the density structures of the clouds; yet its usage is usually limited to spherically symmetric systems. Importing the Level-Set Method, we develop a new formalism that generates robust maps of a generalized density exponent kρ at every location for complex density distributions. By applying it to high fidelity, high dynamical range map of the Perseus molecular cloud constructed using data from the Herschel and Planck satellites, we find that the density exponent exhibits a surprisingly wide range of variation (−3.5 ≲ kρ ≲ −0.5). Regions at later stages of gravitational collapse are associated with steeper density profiles. Inside a region, gas located in the vicinities of dense structures has very steep density profiles with kρ ≈ −3, which forms because of depletion. This density exponent analysis reveals diverse density structures, forming a coherent picture that gravitational collapse leads to a continued steepening of the density profile. We expect our method to be effective in studying other power law-like density structures, including granular materials and the large-scale structure of the Universe.
Discovery of a coherent, wave-like velocity pattern for the Radcliffe wave
Authors: Li Guang-Xing , Chen Bing-Qiu 
Published: May 2022

ABSTRACT
Recent studies discovered that part of the Gould Belt belongs to a 2.7 kpc-long coherent, thin wave consisting of a chain of clouds, where a damped undulation pattern has been identified from the spatial arrangement of the clouds. We use the proper motions of young stellar objects anchored inside the clouds to study the kinematic structure of the Radcliffe wave in terms of vz, and identify a damped, wave-like pattern from the vz space, which we call ‘velocity undulation’. We propose a new formalism based on the ensemble empirical mode decomposition to determine the amplitude, period, and phase of the undulation pattern, and find that the spatial and velocity undulation share an almost identical spatial frequency of about 1.5 kpc, and both are damped when measured from one side to the other. Measured for the first cycle, they exhibit a phase difference of around 2π/3. The structure is oscillating around the mid-plane of the Milky Way disc with an amplitude of ${\sim}130\, \pm \, 20\, \rm pc$. The vertical extent of the Radcliffe wave exceeds the thickness of the molecular disc, suggesting that the undulation of the undulation signature might originate from a perturbation, e.g. the passage of a dwarf galaxy.
Organizational Practice and Neighborhood Context of Racial Inequality in Police Use-of-Force
Authors: Omori Marisa , Lautenschlager Rachel , Stoler Justin 
Published: May 2022

Abstract
Recent highly-publicized cases of police violence have raised broader discussions around understanding use-of-force as institutional racism. We explore how variation in police practices, including discretionary stops and targeting outdoor spaces, along with racialized understandings of crime and space, help explain use-of-force in neighborhoods. Using stop-and-frisk data from the New York City Police Department (NYPD) in Census tracts (N = 12675) between 2006 and 2012, we conduct a spatial analysis and estimate multilevel negative binomial regression models. We find relationships between use-of-force incidents and police organizational practices, where police use force more often in neighborhoods where they employ greater discretionary stops, and in neighborhoods where police conduct proportionally more indoor stops. Our findings also point to understanding stop-and-frisk as a spatial strategy concentrated largely in neighborhoods of color, where police use force more often in Black and Latinx neighborhoods above and beyond the racial disproportionately of individuals stopped. Police also use force more often in neighborhoods where they perceive more crime, even after accounting for the observed crime rate. We suggest that use-of-force by the NYPD is systematically produced through organizational practices paired with shared racialized understandings of crime and space that vary across neighborhoods.
Advantageous effect of pupil dilation on the quality of optical biometry axial length measurement in individuals with dense cataract
Authors: Bettach Emmanuel , Weill Yishay , Aronovitz Yocheved , Zadok David , Gelman Evegeny , Abulafia Adi 
Published: May 2022

Purpose:
To evaluate the effect of pharmacologic pupil dilation on the quality of axial length (AL) measurement in patients with dense cataracts and previous low-quality AL measurements performed without dilation.

Setting:
Shaare-Zedek Medical Center, Jerusalem, Israel.

Design:
Retrospective case series.

Methods:
All participants underwent swept-source optical coherence tomographic (SS-OCT) biometry. Those with low-quality AL measurements due to dense cataract underwent an additional SS-OCT biometric evaluation after pupil dilation, and the AL measurement of the same eye was recorded.

Results:
2076 patients underwent SS-OCT during the study period, and 177 (8.52%) had low-quality AL measurements because of dense cataract. 79 (44.63%, mean age 72.53 ± 13.27 years, 43 females) of those 177 patients underwent repeat SS-OCT biometric imaging after pharmacologic pupil dilation, and formed the study group. After pupil dilation, high-quality AL measurements were successfully obtained in 60 (75.95%) of the 79 eyes. The mean SD of the AL measurements decreased significantly (P < .001), and the number of successful OCT scans per measurement increased significantly (P < .001) after pupil dilation. The mean difference of the AL before and after pupil dilation was 0.03 ± 0.07 mm (P < .001).

Conclusions:
Pharmacologic pupil dilation improved the quality of SS-OCT biometrically measured AL in patients with low-quality AL measurement due to dense cataract. These results could potentially improve postoperative refractive outcomes after cataract surgery and reduce the need of additional AL measurements by more complicated alternative means in this group.
Production of a Low-Cost, Off-the-Shelf, Decellularized Cartilage Xenograft for Tissue Regeneration
Authors: Vernice Nicholas A. , Berri Nabih , Bender Ryan J. , Dong Xue , Spector Jason A. 
Published: May 2022

Background
Reconstruction of cartilaginous deformities is a well-established surgical challenge with high levels of unpredictability and complication. Because of the morbidity associated with autologous cartilage grafting, combined with its limited supply and the significant expense of commercially decellularized allografts, increasing efforts have sought to produce an acellular, nonimmunogenic cartilage xenograft. We have developed and validated a novel protocol for high throughput decellularization of ovine costal cartilage with immediate translational potential for preclinical investigation of novel strategies for cartilaginous reconstruction.

Methods
Floating ribs were isolated from freshly slaughtered rack of lamb and after cleaning, the ribs were either minced into 2-mm cubes or zested into 1-mm flakes. Tissue was then decellularized via a protocol consisting of 4 freeze/thaw cycles, digestion with trypsin, incubation in hyperosmolar and hypoosmolar salt solutions, with incubation in 1% Tween following both the hyperosmolar and hypoosmolar steps, a 48-hour incubation in nucleases, DNA elution via EDTA, and 2 terminal sterilization steps. Protocol success was evaluated via histologic analysis with hematoxylin and eosin, DAPI, and safranin-O staining, as well as DNA quantification.

Results
Histologic analysis of the decellularized tissue revealed a significant reduction in nuclei as evidenced by hematoxylin and eosin and DAPI staining (P < 0.01). Safranin-O staining demonstrated a depletion of glycosaminoglycan content in the decellularized cartilage but with preservation of tissue architecture. Unprocessed lamb cartilage contained 421 ± 60 ng DNA/mg of lyophilized tissue, whereas decellularized zested and minced costal cartilage contained 27 ± 2 ng DNA/mg lyophilized tissue (P < 0.0001) and 24 ± 2.3 ng DNA/mg lyophilized tissue (p < 0.0001), respectively, well below the threshold of 50 ng accepted as evidence of suitable decellularization. In comparison, commercial allograft cartilage contained 17 ± 5 ng DNA/mg of lyophilized tissue.

Conclusions
We have developed a novel protocol for the decellularization of xenogeneic cartilage graft. This structurally stable, low immunogenicity decellularized cartilage can be produced at low cost in large quantities for use in preclinical investigation.
The spread and burden of the COVID-19 pandemic in sub-Saharan Africa: comparison between predictions and actual data and lessons learned
Authors: Fokoua-Maxime Christophe Dongmo , Bellouche Yahia , Tchigui-Ariolle Dillonne Ngonpong , Tchato-Yann Tchana Loic , Choukem Simeon Pierre 
Published: May 2022

ABSTRACTIntroductionSub-Saharan Africa (SSA) was predicted to be severely affected by the coronavirus disease 2019 (COVID-19) pandemic, but the actual data seem to have contradicted these forecasts. This study attempted to verify this observation by comparing predictions against actual data on the spread and burden of the COVID-19 pandemic in SSA.MethodsFocused on the period from March 1stto September 30th, 2020, we compared (1) the predicted interval dates when each SSA country would report 1 000 and 10 000 COVID-19 cases, to the actual dates when these numbers were attained, as well as (2) the daily number of predicted versus actual COVID-19 cases.Further, we calculated the case fatality ratio of the COVID-19 infection in SSA, and the correlation coefficient between the weekly average number of confirmed COVID-19 cases reported by each country and the weekly average stringency index of its anti-COVID-19 policy measures.Results84.61% (33) and 100% (39) of the 39 SSA countries for which predictions were made did not reach a total of 1 000 and 10 000 confirmed COVID-19 cases at the predicted interval dates. The daily number of confirmed COVID-19 cases was lower than the one projected for all SSA countries. The case fatality ratio of the COVID-19 infection in SSA was 3.42%. Among the 44 SSA countries for which the correlation could be estimated, it was negative for 17 (38.6 %) of them.ConclusionsThe natural characteristics of SSA and the public health measures implemented might partly explain that the actual data were lower than the predictions on the COVID-19 pandemic in SSA, but the low case ascertainment and the numerous asymptomatic cases did significantly influence this observation.
Compartment-Specific Measurement of Small Molecule Accumulation into Diderm Bacteria
Authors: Ongwae George M. , Lepori Irene , Chordia Mahendra D. , Dalesandro Brianna E. , Apostolos Alexis J. , Siegrist M. Sloan , Pires Marcos M. 
Published: May 2022

AbstractSome of the most dangerous bacterial pathogens (Gram-negative and mycobacterial) deploy a formidable secondary membrane barrier to reduce the influx of exogenous molecules. For Gram-negative bacteria, this second exterior membrane is known as the outer membrane, while for the Gram-indeterminate Mycobacteria, it is known as the ‘myco’ membrane. Although different in composition, both the outer membrane and mycomembrane are key structures that restrict the passive permeation of small molecules into bacterial cells. While it is well-appreciated that such structures are principal determinants of small molecule permeation, it has proven to be challenging to assess this feature in a robust and quantitative way or in complex, infection-relevant settings. Herein, we describe the development of the Bacterial Chloro-Alkane Penetration Assay (BaCAPA), which employs the use of a genetically encoded protein called HaloTag, to measure the uptake and accumulation of molecules into model Gram-negative and mycobacterial species, Escherichia coli and Mycobacterium smegmatis, respectively, and into the human pathogen M. tuberculosis. Directing the localization of the HaloTag protein to either the cytoplasm or periplasm of bacteria enabled a compartmental analysis of permeation across individual cell membranes. Significantly, we also showed that BaCAPA can be used to analyze the permeation of molecules into host cell-internalized E. coli and M. tuberculosis, a critical capability for analyzing intracellular pathogens. Together, our results show that BaCAPA affords facile, compartment-specific measurement of permeability across four barriers: the host plasma and phagosomal membranes and the diderm bacterial cell envelope.