bluuebunny/crossref_metadata_2025 huggingface dataset:
Usefulness of optical enhancement endoscopy combined with magnification to improve detection of intestinal metaplasia in the stomach
Authors: Sobrino-Cossío Sergio , Teramoto-Matsubara Oscar , Emura Fabian , Araya Raúl , Arantes Vítor , Galvis-García Elymir S. , Meza-Caballero Marisi , García-Aguilar Blanca Sinahi , Reding-Bernal Arturo , Uedo Noriya
Published: April 2022

Background and study aims The light blue crest observed in narrow band imaging endoscopy has high diagnostic accuracy for diagnosis of gastric intestinal metaplasia (GIM). The objective of this prospective study was to evaluate the diagnostic accuracy of magnifying i-scan optical enhancement (OE) imaging for diagnosing the LBC sign in patients with different levels of risk for gastric cancer in a Mexican clinical practice.

Patients and methods Patients with a history of peptic ulcer and symptoms of dyspepsia or gastroesophageal reflux disease were enrolled. Diagnosis of GIM was made at the predetermined anatomical location and white light endoscopy and i-scan OE Mode 1 were captured at the two predetermined biopsy sites (antrum and pyloric regions).

Results A total of 328 patients were enrolled in this study. Overall GIM prevalence was 33.8 %. The GIM distribution was 95.4 % in the antrum and 40.5 % in the corpus. According to the Operative Link on Gastritis/Intestinal-Metaplasia Assessment staging system, only two patients (1.9 %) were classified with high-risk stage disease. Sensitivity, specificity, positive​ and negative predictive values, positive and negative likelihood ratios, and accuracy of both methods (95 % C. I.) were 0.50 (0.41–0.60), 0.55 (0.48–0.62), 0.36 (0.31–0.42), 0.68 (0.63–0.73), 1.12 (0.9–1.4), 0.9 (0.7–1.1), and 0.53 (0.43–0.60) for WLE, and 0.96 (0.90–0.99), 0.91 (0.86–0.94), 0.84 (0.78–0.89), 0.98 (0.94–0.99), 10.4 (6.8–16), 0.05 (0.02–0.12), and 0.93 (0.89–0.95), respectively. The kappa concordance was 0.67 and the reliability coefficient was 0.7407 for interobserver variability.

Conclusions Our study demonstrated the high performance of magnifying i-scan OE imaging for endoscopic diagnosis of GIM in Mexican patients.
Effects of a Multicomponent Exercise Training Program on Balance
Following Bariatric Surgery
Authors: Diniz-Sousa Florêncio , Granja Tiago , Boppre Giorjines , Veras Lucas , Devezas Vítor , Santos-Sousa Hugo , Preto John , Machado Leandro , Vilas Boas Joao Paulo , Oliveira Jose , Fonseca Hélder
Published: April 2022

Patients who undergo bariatric surgery (BS) have an increased risk of falls. Our
aim was to determine if a multicomponent exercise intervention after BS improves
balance. Eighty-four patients with obesity enrolled for BS were recruited and 1
month after BS randomly allocated to a control (CG; standard medical care) or
exercise group (EG; exercise plus standard medical care) consisting of a
supervised multicomponent training program (3d/week; 75
min/session; 5 months). Anthropometry, lower limb muscle strength
(isokinetic dynamometer), vitamin D (ELISA) and balance in bipedal stance (force
platform) were assessed pre-BS, 1 month and 6 months post-BS. One month post-BS,
significant balance improvements were observed, namely in antero-posterior
center of gravity (CoG) displacement and velocity, and medio-lateral and total
CoG velocity. Between 1- and 6-months post-BS, improvements in balance were
observed only in the EG, with a significant treatment effect on CoG displacement
area and antero-posterior CoG displacement. No significant differences were
observed between EG and CG over time in any of the anthropometric, muscle
strength, and vitamin D variables assayed. In conclusion, a multicomponent
exercise intervention program improves some balance parameters in patients with
severe obesity following BS and therefore should be part of post-BS follow-up
care as a potential strategy to reduce falls and associated injuries.
Kutane Sarkome – nicht alle sind wirklich selten, die meisten „low risk“
Authors: Vogt Thomas
Published: April 2022

Die biologische und morphologische Vielfalt der Weichteilmalignome, der Sarkome, ist enorm.

Diese Übersicht fokussiert deshalb auf die 5 am häufigsten vorkommenden Weichteilmalignome. Betrachtet werden soll dabei, was der Kliniker wissen muss, was neu ist und welche Fallstricke es gibt. Ziel dieses Artikels ist es dabei, eine Übersicht zu geben sowie die Konzeptbildung darüber, womit man es im Wesentlichen zu tun hat.
Digestive perforations related to endoscopy procedures: a local management charter based on local evidence and experts’ opinion
Authors: Bertrand Gaspard , Rivory Jérôme , Robert Maud , Saurin Jean-Christophe , Pelascini Élise , Monneuse Olivier , Gruner Laurent , Poncet Gilles , Valette Pierre-Jean , Gimonet Hélène , Rostain Florian , Ber Charles-Éric , Bouffard Yves , Boibieux André , Ciochina Marina , Landel Verena , Boyer Hélène , Jacques Jérémie , Ponchon Thierry , Pioche Mathieu
Published: April 2022

Background and study aims Perforations are a known adverse event of endoscopy procedures; a proposal for appropriate management should be available in each center as recommended by the European Society of Gastrointestinal Endoscopy. The objective of this study was to establish a charter for the management of endoscopic perforations, based on local evidence.

Patients and methods Patients were included if they experienced partial or complete perforation during an endoscopic procedure between 2008 and 2018 (retrospectively until 2016, then prospectively). Perforations (size, location, closure) and management (imagery, antibiotics, surgery) were analyzed. Using these results, a panel of experts was asked to propose a consensual management charter.

Results A total of 105 patients were included. Perforations occurred mainly during therapeutic procedures (91, 86.7%). Of the perforations, 78 (74.3 %) were diagnosed immediately and managed during the procedure; 69 of 78 (88.5 %) were successfully closed. Closures were more effective during therapeutic procedures (60 of 66, 90.9 %) than during diagnostic procedures (9 of 12, 75.0 %, P = 0.06). Endoscopic closure was effective for 37 of 38 perforations (97.4 %) < 0.5 cm, and for 26 of 34 perforations (76.5 %) ≥ 0.5 cm (P < 0.05). For perforations < 0.5 cm, systematic computed tomography (CT) scan, antibiotics, or surgical evaluation did not improve the outcome. Four of 105 deaths (3.8 %) occurred after perforation, one of which was attributable to the perforation itself.

Conclusions Detection and closure of perforations during endoscopic procedure had a better outcome compared to delayed perforations; perforations < 0.5 cm had a very good prognosis and CT scan, surgeon evaluation, or antibiotics are probably not necessary when the endoscopic closure is confidently performed. This work led to proposal of a local management charter.
Efficiency of an endoscopic resection strategy for management of submucosal tumors < 20 mm in the upper gastrointestinal tract
Authors: Caillol Fabrice , Meunier Elise , Zemmour Christophe , Ratone Jean-Philippe , Guiramand Jerome , Hoibian Solene , Dahel Yanis , Poizat Flora , Giovannini Marc
Published: April 2022

Background and study aims The histologic diagnosis of submucosal tumors (SMTs) < 20 mm is challenging. Monitoring is the main option offered, but compliance is debatable. Endoscopic resection (ER) of malignant SMTs or those with an uncertain diagnosis is an alternative that has already been reported about and proposed in our center. The aims of this study were to confirm the safety of this resection strategy and to perform long-term follow-up of malignant SMTs after resection.

Patients and methods All patients who underwent ER for SMTs < 2 cm in a single center between 2007 and 2019 were included retrospectively. Patients were classified into two groups according to the need for postresection follow-up: benign SMTs (B-SMTs) and follow-up SMTs (FU-SMTs).

Results One hundred and one patients were included. The mean tumor size was 16.7 mm. In total, 92 of 101 SMTs had an uncertain diagnosis. Macroscopic resection was completed for 95 SMTs (93.1 %), with en bloc resection in 94 (92.1%). The morbidity rate was 3 %, with no mortality. A total of 84 of 101 SMTs (84 %) were B-SMTs and did not need monitoring, and 17 SMTs (19.7 %) were FU-SMTs (8 gastrointestinal stromal tumors, 6 neuroendocrine tumors, and 3 others). No relapse was reported in the FU-SMT group, with a median follow-up duration of 33 months [4–127] (61 months [17–127] for the gastrointestinal stroma tumor group).

Conclusions The study results suggest ER is a potentially reliable and effective strategy for upper gastrointestinal tract SMTs < 20 mm. Although the strategy needs further validation in advanced care units, it could eliminate the need for long-term monitoring, therefore targeting such follow-up efforts to patients with FU-SMTs.
Endoscopy-induced anterior cutaneous nerve entrapment syndrome: a case series
Authors: Wolfhagen Frank H.J.
Published: April 2022

Background and study aims Anterior cutaneous nerve entrapment syndrome (ACNES) is a common but frequently overlooked disorder. Here we report on a series of patients with ACNES following endoscopy.

Patients and methods This case series included consecutive patients with localized abdominal pain following an endoscopic procedure that was consistent with ACNES who presented to the author’s Gastroenterology Outpatient Clinic from February 2019 to February 2021.

Results Six patients presented with complaints compatible with ACNES. All of them were successfully managed with local injection therapy (n = 5) or pulsed radiofrequency (PRF) (n = 1).

Conclusions It appears that ACNES can be induced by endoscopy. Early recognition is important to avoid unnecessary diagnostics and delayed pain relief in patients. Most patients can be managed with local injection therapy.
Cephalic Vein Aneurysm in the Distal Forearm Managed with Sclerotherapy—A Rare Case Report and Literature Review
Authors: Mahajan Ashima , Fazal Syed T. , Mehta Sanjay , Kataria Narender S. , Nanda Vipul
Published: April 2022

Venous aneurysm of upper extremities is rare entity. We report a rare case of large cephalic vein (CV) aneurysm in a 41-year-old man who presented as slowly growing painless swelling at distal forearm along the lateral aspect. Duplex ultrasound showed aneurysm originating from the anterior wall of the CV with venous waveform pattern on Doppler. It was managed successfully with percutaneous sclerotherapy.
Effects of Electrode Location on Speech Recognition with the Nucleus-22 Cochlear Implant
Authors: Friesen Lendra M. , Shannon Robert V. , Slattery William H.
Published: April 2022

Speech recognition performance was measured as a function of electrode in two experiments with the Nucleus-22 cochlear implant using 4–electrode SPEAK speech processors. In experiment 1, the four stimulated electrode pairs were shifted in 0.75–mm steps over 3 mm in the apical-basal direction. In experiment 2, the four electrodes were closely spaced and positioned apically, medially, or basally. An additional condition spaced the four electrodes as widely as possible. In experiment 1, City University of New York sentence scores showed a significant decrease in performance as the electrodes were shifted basally; no other speech measures showed a significant change with electrode location. For experiment 2, all scores were the best with the processor that had the electrodes spaced as widely as possible. In both experiments, all 4–electrode SPEAK processors produced significantly poorer speech recognition than the subject's own 20–electrode processor. These results indicate that the location of electrodes is an important factor in implant performance.

Abbreviations: C = maximum comfortable loudness levels, CI = cochlear implant, CUNY = City University of New York, NU-6 = Northwestern University Auditory Test No. 6, Τ = electrical thresholds
Report of the Consensus Conference on the Diagnosis of Auditory Processing Disorders in School-Aged Children
Authors: Jerger James , Musiek Frank
Published: April 2022

BACKGROUND

A group of 14 senior scientists and clinicians met at the Callier Center in Dallas over the 2–day period, April 27–28, 2000, in an attempt to reach a consensus on the problem of diagnosing auditory processing disorders in school-aged children. The conference was organized by James Jerger and Frank Musiek. The following individuals participated:

Sharon Abel, PhD, University of Toronto, Toronto, ON

Jane Baran, PhD, University of Massachusetts, Amherst, MA

Anthony Cacace, PhD, Albany Medical College, Albany, NY

Gail Chermak, PhD ‡, Washington State University, Pullman, WA

Susan Dalebout, PhD, University of Virginia, Charlottesville,VA

Jay Hall III, PhD, University of Florida, Gainesville, FL

Linda Hood, PhD, Louisiana State University Medical Center, New Orleans, LA

Lisa Hunter, PhD, University of Minnesota, Minneapolis, MN

James Jerger, PhD, University of Texas at Dallas, Dallas, TX

Susan Jerger, PhD, University of Texas at Dallas, Dallas, TX

Robert Keith, PhD, University of Cincinnati, Cincinnati, OH

Frank Musiek, PhD, Dartmouth-Hitchcock Medical Center, Hanover, NH

Ross Roeser, PhD, University of Texas at Dallas, Dallas, TX

Christine Sloan, PhD, Annapolis Valley Regional School Board Berwick, NS

Meeting both as separate groups and in plenary session, the conferees reached the consensus summarized below.
The teaching of the cello in Spain: An analysis of the planning frameworks used for teaching in conservatories
Authors: Hernández-Dionis Paula , Pérez-Jorge David , Gisbert-Caudeli Vicenta , de la Rosa Olga María Alegre
Published: April 2022

One might think that the elementary teachings of an instrument should follow uniform planning patterns. The present study shows discrepancies between the models developed by different Spanish conservatories, mainly attributable to the guidelines established by each autonomous community concerning the order of the curriculum markedly influenced by each community’s circumstances. This article analyzes and compares first-year didactic programs in the elementary music teachings of 40 Spanish conservatories within the cello specialty. This work shows significant heterogeneity in planning, marked mainly by the variety of content in planning. The lack of unified criteria and standards for teaching planning is evident in teachers’ freedom to establish the contents and evaluation criteria within the framework of regulations in each autonomous community, whose generality prevents the establishment of standard criteria. It is urgent and necessary to design training plans and standard content that consider improved learning practices and strategies to offer quality training based on common standards.
An efficient implementation of time-dependent linear-response theory for strongly orthogonal geminal wave function models
Authors: Hapka Michał , Pernal Katarzyna , Jensen Hans Jørgen Aa.
Published: April 2022

We present an implementation of time-dependent linear-response equations for strongly orthogonal geminal wave function models: the time-dependent generalized valence bond (TD-GVB) perfect-pairing theory and the antisymmetrized product of strongly orthogonal geminals. The geminal wave functions are optimized using a restricted-step second-order algorithm suitable for handling many geminals, and the linear-response equations are solved in an efficient way using a direct iterative approach. The wave function optimization algorithm features an original scheme to create initial orbitals for the geminal functions in a black-box fashion. The implementation is employed to examine the accuracy of the geminal linear response for singlet excitation energies of small and medium-sized molecules. In systems dominated by dynamic correlation, geminal models constitute only a minor improvement with respect to time-dependent Hartree–Fock. Compared to the linear-response complete active space self-consistent field, TD-GVB either misses or gives large errors for states dominated by double excitations.
On metric properties of $C$-capacities associated with solutions of second-order strongly elliptic equations in $\pmb{\mathbb R}^2$
Authors: Paramonov Petr Vladimirovich
Published: April 2022

For certain capacities that were used previously to formulate criteria for the uniform approximability of functions by solutions of strongly elliptic equations of the second order on compact subsets of $\mathbb R^2$, a number of metric properties are established. New, more natural criteria for individual approximability are obtained as consequences. Unsolved problems of interest are stated.
Bibliography: 13 titles.
An upper bound for the least critical values of finite Blaschke products
Authors: Dubinin Vladimir Nikolaevich
Published: April 2022

For the finite Blaschke products $B$ of degree $n\geqslant2$ such that $B(0)=0$ and $ B'(0)\ne0$, the supremum of the minimum moduli of their critical values is found which depends only on $n$ and $|B'(0)|$.
Bibliography: 12 titles.
Legal Status of Recreational Cannabis and Self-Reported Substitution of Cannabis for Opioids or Prescription Pain Medication in Canada and the United States
Authors: Wadsworth Elle , Hines Lindsey A. , Hammond David
Published: April 2022

Aims: With increased liberalization of cannabis policies in North America, there is growing interest in the use of cannabis to manage pain instead of opioids. The objectives of the study were to (1) examine the use of cannabis for pain relief in Canada and the United States (US) in 2018 and 2019; (2) examine the association between recreational cannabis laws and changes in the use of cannabis for pain relief, instead of opioids or prescription pain medication. Methods: Repeat cross-sectional survey data were used from Wave 1 and Wave 2 of the International Cannabis Policy Study conducted in 2018 and 2019 in Canada and the US. Respondents were recruited through commercial panels, aged 16–65, and had ever tried cannabis ( N = 44,119). Weighted binary logistic regression models examined the association between the legal status of recreational cannabis and cannabis use for pain relief instead of opioids or prescription pain medication ( n = 15,092). Results: Between 14–33% of cannabis consumers in Canada and the US reported using cannabis to manage headaches or pain. Of these consumers, 79% and 78% respondents in Canada; 80% and 83% in US illegal states; and 83% and 84% in US legal states, in 2018 and 2019, respectively, reported cannabis use for pain relief instead of opioids or prescription pain medication. There was little evidence of an association between the legal status of recreational cannabis and cannabis use for pain relief instead of opioids or prescription pain medication, among Canadian (AOR = 0.98, 95% CI: 0.78, 1.22) and US respondents (AOR = 1.11, 95% CI: 0.96, 1.28). Conclusions: Although substitution of cannabis for opioids or prescription pain medication is common among those who use cannabis for pain, there does not seem to be a significant difference according to cannabis legality. Future research should examine cannabis and opioid substitution using different research designs and time frames.
Factors Associated with Binge Drinking—Findings from 2019 Kansas Behavioral Risk Factor Surveillance System
Authors: Lines Shannon R. , Marroquin Aliya , Corbett Steve , Sergeant Julie , Choi Won , Faseru Babalola
Published: April 2022

Background: In the U.S., excessive drinking accounts for one in 10 deaths among adults aged 20–64 years old. Binge drinking is a common form of excessive alcohol consumption that contributes to this chilling statistic. Binge drinking is defined as women consuming four or more drinks or men consuming five or more drinks within a 2-h time span. Examining existing data on risk factors for binge drinking can inform strategies to prevent this deadly practice. Methods: The 2019 Kansas Behavioral Risk Factor Surveillance System (BRFSS) dataset consists of data collected from 11,368 non-institutionalized adults aged 18 years and older with landline or cell phones. The dependent variable in this study was binge drinking status. The independent variables included several sociodemographic variables and risk factors. Data were analyzed using descriptive statistics, bivariate analysis, single logistic regression, and multivariable logistic regression. Results: In the population, 1,447 (17.4%) were reported to be binge drinkers. Significant factors associated with binge drinking in the final model included sex (aOR = 0.53 (0.45–0.63)), age (18–24 years old aOR = 8.77 (6.02–12.79); 25–34 years old aOR = 7.10 (5.35–9.42); 35–44 years old aOR = 6.23 (4.73–8.19); 45–54 years old aOR = 3.87 (2.92–5.14); and 55–64 years old aOR = 2.58 (1.96–3.38)), income ($15,000–$24,999 aOR = 1.00 (0.63–1.58); $25,000–$34,999 aOR = 1.61 (1.04–2.50); $35,000-$49,999 aOR = 1.69 (1.13–2.55); ≥$50,000 aOR = 1.97 (1.34–2.89)), smokeless tobacco use (aOR = 2.09 (1.55–2.82)), and smoking/e-cigarette use (Cigarette user only aOR = 2.11 (1.69–2.65); E-cigarette user only aOR = 2.67 (1.62–3.17); dual cigarette and e-cigarette user = 3.43 (2.21–5.33)). Conclusion: Developing interventions that take into account elevated risk for binge drinking amongst demographic characteristics (i.e., age, sex, income) and lifestyle factors (i.e., smokeless tobacco use, and smoking/e-cigarette use) is crucial to lowering morbidity and mortality related to this form of excessive alcohol consumption.
SARS-CoV-2 infection relaxes peripheral B cell tolerance
Authors: Castleman Moriah J. , Stumpf Megan M. , Therrien Nicholas R. , Smith Mia J. , Lesteberg Kelsey E. , Palmer Brent E. , Maloney James P. , Janssen William J. , Mould Kara J. , Beckham J. David , Pelanda Roberta , Torres Raul M.
Published: April 2022

Severe SARS-CoV-2 infection is associated with strong inflammation and autoantibody production against diverse self-antigens, suggesting a system-wide defect in B cell tolerance. BND cells are a B cell subset in healthy individuals harboring autoreactive but anergic B lymphocytes. In vitro evidence suggests inflammatory stimuli can breach peripheral B cell tolerance in this subset. We asked whether SARS-CoV-2–associated inflammation impairs BND cell peripheral tolerance. To address this, PBMCs and plasma were collected from healthy controls, individuals immunized against SARS-CoV-2, or subjects with convalescent or severe SARS-CoV-2 infection. We demonstrate that BND cells from severely infected individuals are significantly activated, display reduced inhibitory receptor expression, and restored BCR signaling, indicative of a breach in anergy during viral infection, supported by increased levels of autoreactive antibodies. The phenotypic and functional BND cell alterations significantly correlate with increased inflammation in severe SARS-CoV-2 infection. Thus, autoreactive BND cells are released from peripheral tolerance with SARS-CoV-2 infection, likely as a consequence of robust systemic inflammation.
The magnetic structure of DyFeO3 revisited: Fe spin reorientation and Dy incommensurate magnetic order
Authors: Ritter Clemens , Vilarinho Rui , Moreira Joaquim Agostinho , Mihalik Matus , Mihalik Marian , Savvin Stanislav
Published: April 2022

High resolution and high intensity neutron powder diffraction is used to study the ground state magnetic order and the spin reorientation transition in the orthoferrite DyFeO3. The transition from the high temperature k = 0 Γ4 (G

x

A

y

F

z
) to the low temperature Γ1 (A

x

G

y

C

z
) type order of the Fe-sublattice is found at T
SR = 73 K and does not show any thermal hysteresis. Below T
N2 = 4 K the Dy-sublattice orders in an incommensurate magnetic structure with k = [0, 0, 0.028] while the Fe-sublattice keeps its commensurate Γ1 type order. DyFeO3 is the first orthoferrite RFeO3 to possess an incommensurate magnetic order of the rare earth sublattice under zero field conditions; an important piece of information neglected in the recent discussion of its multiferroic properties.
Quantum statistics of phonon radiations in optomechanical systems
Authors: Chen Menghan , Chang Yue , Shi Tao
Published: April 2022

We study the correlation statistics of phonon radiations in a weakly driven optomechanical system. Three dominated scattering processes are identified by the scattering theory analytically and the master equation numerically, whose interplay determines the phonon statistical properties. Our results show that for the large detuning, the driving field off-resonant with the system induces a small emission rate of two anti-bunched phonons. For the resonant driving field, there is a relatively large emission rate of two bunched phonons.
Generating images of hydrated pollen grains using deep learning
Authors: Grant-Jacob James A , Praeger Matthew , Eason Robert W , Mills Ben
Published: April 2022

Pollen grains dehydrate during their development and following their departure from the host stigma. Since the size and shape of a pollen grain can be dependent on environmental conditions, being able to predict both of these factors for hydrated pollen grains from their dehydrated state could be beneficial in the fields of climate science, agriculture, and palynology. Here, we use deep learning to transform images of dehydrated Ranunculus pollen grains into images of hydrated Ranunculus pollen grains. We also then use a deep learning neural network that was trained on experimental images of different genera of pollen grains to identify the hydrated pollen grains from the generated transformed images, to test the accuracy of the image generation neural network. This pilot work demonstrates the first steps needed towards creating a general deep learning-based rehydration model that could be useful in understanding and predicting pollen morphology.
The carbon footprint of cold chain food flows in the United States
Authors: Wang Junren , Karakoc Deniz Berfin , Konar Megan
Published: April 2022

The food system is an important contributor to carbon dioxide (CO2) emissions. The refrigerated food supply chain is an energy-intensive, nutritious and high-value part of the food system, making it particularly important to consider. In this study, we develop a novel model of cold chain food flows between counties in the United States. Specifically, we estimate truck transport via roadways of meat and prepared foodstuffs for the year 2017. We use the roadway travel distance in our model framework rather than the haversine distance between two locations to improve the estimate for long-haul freight with a temperature-controlled system. This enables us to more accurately calculate the truck fuel consumption and CO2 emissions related to cold chain food transport. We find that the cold chain transport of meat emitted 8.4 × 106 t CO2 yr−1 and that of prepared foodstuffs emitted 14.5 × 106 t CO2 yr−1, which is in line with other studies. Meat has a longer average refrigerated transport distance, resulting in higher transport CO2 emissions per kg than processed foodstuffs. We also find that CO2 emissions from cold chain food transport are not projected to significantly increase under the temperatures projected to occur with climate change in 2045. These county-level cold chain food flows could be used to inform infrastructure investment, supply chain decision-making and environmental footprint studies.
Less Incorrect Ways of Doing Jurisprudence
Authors: Fasel Raffael N
Published: April 2022

Theorists interested in the question of how to do jurisprudence often have the aspiration of developing a method that is the correct one. The article challenges this aspiration. Focusing on Julie Dickson’s claim that Indirectly Evaluative Legal Theory is the correct method, I show that any method claiming to be the correct one runs into the problem that law is not the kind of thing that a legal theorist could capture independently of her underlying conception of law, and without potentially influencing what law is through her own theory. However, this does not spell the end of jurisprudential methodology. The article proposes that methodologists should shift their focus away from the pursuit of single correct methods and toward studying and weeding out incorrect methods. I outline some of the principles that theorists can use for this purpose and point to promising avenues of research that this shift opens up.
Effects of honeybee (Apis cerana) visiting behaviour on toxic plant (Tripterygium hypoglaucum) reproduction
Authors: Chen Shunan , Wang Yunfei , Li Yi , Zhang Xuewen , Wu Jie
Published: April 2022

Honeybees play a significant role in the plant–pollinator interactions of many flowering plants. The ecological and evolutionary consequences of plant–pollinator interactions vary by geographic region, and the effects of honeybees on the reproduction of toxic plants have not been well studied. We measured the florescence of toxic plants, the flower-visiting behaviour of honeybees and the effects of pollination on the fertility, weight and moisture content of seeds. The effects of climatic factors on the number of flowers, and the spatial and temporal variation in pollinator visits were evaluated, and the effects of pollinator visits on seed quality were evaluated. Flower visitors were diverse, climatic factors had a great impact on spatio-temporal flowering variation and the number of bee visits was strongly correlated with the spatio-temporal variation in the number of flowers. Honeybees strongly increase the fullness and weight of seeds. Our study demonstrated a good ecological fit between the spatio-temporal variation in the flowering of toxic plants and the general validity of honeybee pollination syndrome in the south of Hengduan Mountains in East Asia. A linear relationship between honeybee visitation and plant reproduction can benefit the stabilization of plant reproduction.
Assessing Preseason Baseline Cognitive Functioning in High School Student Athletes: A “Hybrid” Approach
Authors: Ransom Danielle M , Ahumada Luis , Amankwah Ernest K , Katzenstein Jennifer M , Goldenberg Neil A , Mularoni P Patrick
Published: April 2022

Objective

International consensus statements highlight the value of neuropsychological testing for sport-related concussion. Computerized measures are the most frequently administered assessments of pre-injury baseline and post-injury cognitive functioning, despite known measurement limitations. To our knowledge, no studies have explored the convergent validity of computerized Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) and traditional, well-validated paper and pencil (P&P) neuropsychological tests in high school student athletes. This study aimed to assess a “hybrid” adolescent test battery composed of ImPACT and P&P measures to determine the extent of shared variance among ImPACT and P&P tests to inform comprehensive yet streamlined assessment.

Method

Participants included male and female high school student athletes in the Southeastern United States participating in American football, hockey, and soccer who completed a battery of ImPACT and P&P tests (N = 69).

Results

We performed principal component analysis with ProMax rotation to determine components of the hybrid battery that maximally accounted for observed variance of the data (Kaiser–Meyer–Olkin factor adequacy = 0.71). Our analysis revealed four independent factors (Verbal Learning and Memory, ImPACT Memory and Speed, Verbal Processing Speed/Executive Functions, and Nonverbal Processing Speed/Executive Functions) explaining 75% of the variance.

Conclusions

Findings of this study in adolescent student athletes support those from the adult literature demonstrating the independence of ImPACT and P&P tests. Providers should be aware of limitations in using standalone ImPACT or P&P measures to evaluate cognitive functioning after concussion. If confirmed in a larger, clinical sample, our findings suggest that a hybrid battery of computerized and P&P measures provides a broad scope of adolescent cognitive functioning to better inform recovery decisions, including return to play after concussion.
plotsr: visualizing structural similarities and rearrangements between multiple genomes
Authors: Goel Manish , Schneeberger Korbinian
Published: April 2022

Third-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands new tools for visualizing their structural properties. Here, we present plotsr, an efficient tool to visualize structural similarities and rearrangements between genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualization with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density).

Availability and implementation

plotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr).

Supplementary information

Supplementary data are available at Bioinformatics online.
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients
Authors: Fan Bowen , Klatt Juliane , Moor Michael M , Daniels Latasha A ,   Swiss Pediatric Sepsis Study, Agyeman Philipp K A , Berger Christoph , Giannoni Eric , Stocker Martin , Posfay-Barbe Klara M , Heininger Ulrich , Bernhard-Stirnemann Sara , Niederer-Loher Anita , Kahlert Christian R , Natalucci Giancarlo , Relly Christa , Riedel Thomas , Aebi Christoph , Schlapbach Luregn J , Sanchez-Pinto Lazaro N , Agyeman Philipp K A , Schlapbach Luregn J , Borgwardt Karsten M
Published: April 2022

Motivation

Sepsis is a leading cause of death and disability in children globally, accounting for ∼3 million childhood deaths per year. In pediatric sepsis patients, the multiple organ dysfunction syndrome (MODS) is considered a significant risk factor for adverse clinical outcomes characterized by high mortality and morbidity in the pediatric intensive care unit. The recent rapidly growing availability of electronic health records (EHRs) has allowed researchers to vastly develop data-driven approaches like machine learning in healthcare and achieved great successes. However, effective machine learning models which could make the accurate early prediction of the recovery in pediatric sepsis patients from MODS to a mild state and thus assist the clinicians in the decision-making process is still lacking.

Results

This study develops a machine learning-based approach to predict the recovery from MODS to zero or single organ dysfunction by 1 week in advance in the Swiss Pediatric Sepsis Study cohort of children with blood-culture confirmed bacteremia. Our model achieves internal validation performance on the SPSS cohort with an area under the receiver operating characteristic (AUROC) of 79.1% and area under the precision-recall curve (AUPRC) of 73.6%, and it was also externally validated on another pediatric sepsis patients cohort collected in the USA, yielding an AUROC of 76.4% and AUPRC of 72.4%. These results indicate that our model has the potential to be included into the EHRs system and contribute to patient assessment and triage in pediatric sepsis patient care.

Availability and implementation

Code available at https://github.com/BorgwardtLab/MODS-recovery. The data underlying this article is not publicly available for the privacy of individuals that participated in the study.

Supplementary information

Supplementary data are available at Bioinformatics online.
Simulating domain architecture evolution
Authors: Cui Xiaoyue , Xue Yifan , McCormack Collin , Garces Alejandro , Rachman Thomas W , Yi Yang , Stolzer Maureen , Durand Dannie
Published: April 2022

Motivation

Simulation is an essential technique for generating biomolecular data with a ‘known’ history for use in validating phylogenetic inference and other evolutionary methods. On longer time scales, simulation supports investigations of equilibrium behavior and provides a formal framework for testing competing evolutionary hypotheses. Twenty years of molecular evolution research have produced a rich repertoire of simulation methods. However, current models do not capture the stringent constraints acting on the domain insertions, duplications, and deletions by which multidomain architectures evolve. Although these processes have the potential to generate any combination of domains, only a tiny fraction of possible domain combinations are observed in nature. Modeling these stringent constraints on domain order and co-occurrence is a fundamental challenge in domain architecture simulation that does not arise with sequence and gene family simulation.

Results

Here, we introduce a stochastic model of domain architecture evolution to simulate evolutionary trajectories that reflect the constraints on domain order and co-occurrence observed in nature. This framework is implemented in a novel domain architecture simulator, DomArchov, using the Metropolis–Hastings algorithm with data-driven transition probabilities. The use of a data-driven event module enables quick and easy redeployment of the simulator for use in different taxonomic and protein function contexts. Using empirical evaluation with metazoan datasets, we demonstrate that domain architectures simulated by DomArchov recapitulate properties of genuine domain architectures that reflect the constraints on domain order and adjacency seen in nature. This work expands the realm of evolutionary processes that are amenable to simulation.

Availability and implementation

DomArchov is written in Python 3 and is available at http://www.cs.cmu.edu/~durand/DomArchov. The data underlying this article are available via the same link.

Supplementary information

Supplementary data are available at Bioinformatics online.
On the reliability and the limits of inference of amino acid sequence alignments
Authors: Rajapaksa Sandun , Sumanaweera Dinithi , Lesk Arthur M , Allison Lloyd , Stuckey Peter J , Garcia de la Banda Maria , Abramson David , Konagurthu Arun S
Published: April 2022

Motivation

Alignments are correspondences between sequences. How reliable are alignments of amino acid sequences of proteins, and what inferences about protein relationships can be drawn? Using techniques not previously applied to these questions, by weighting every possible sequence alignment by its posterior probability we derive a formal mathematical expectation, and develop an efficient algorithm for computation of the distance between alternative alignments allowing quantitative comparisons of sequence-based alignments with corresponding reference structure alignments.

Results

By analyzing the sequences and structures of 1 million protein domain pairs, we report the variation of the expected distance between sequence-based and structure-based alignments, as a function of (Markov time of) sequence divergence. Our results clearly demarcate the ‘daylight’, ‘twilight’ and ‘midnight’ zones for interpreting residue–residue correspondences from sequence information alone.

Supplementary information

Supplementary data are available at Bioinformatics online.
Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data
Authors: Edrisi Mohammadamin , Valecha Monica V , Chowdary Sunkara B V , Robledo Sergio , Ogilvie Huw A , Posada David , Zafar Hamim , Nakhleh Luay
Published: April 2022

Motivation

Single-nucleotide variants (SNVs) are the most common variations in the human genome. Recently developed methods for SNV detection from single-cell DNA sequencing data, such as SCIΦ and scVILP, leverage the evolutionary history of the cells to overcome the technical errors associated with single-cell sequencing protocols. Despite being accurate, these methods are not scalable to the extensive genomic breadth of single-cell whole-genome (scWGS) and whole-exome sequencing (scWES) data.

Results

Here, we report on a new scalable method, Phylovar, which extends the phylogeny-guided variant calling approach to sequencing datasets containing millions of loci. Through benchmarking on simulated datasets under different settings, we show that, Phylovar outperforms SCIΦ in terms of running time while being more accurate than Monovar (which is not phylogeny-aware) in terms of SNV detection. Furthermore, we applied Phylovar to two real biological datasets: an scWES triple-negative breast cancer data consisting of 32 cells and 3375 loci as well as an scWGS data of neuron cells from a normal human brain containing 16 cells and approximately 2.5 million loci. For the cancer data, Phylovar detected somatic SNVs with high or moderate functional impact that were also supported by bulk sequencing dataset and for the neuron dataset, Phylovar identified 5745 SNVs with non-synonymous effects some of which were associated with neurodegenerative diseases.

Availability and implementation

Phylovar is implemented in Python and is publicly available at https://github.com/NakhlehLab/Phylovar.
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
Authors: Kulmanov Maxat , Hoehndorf Robert
Published: April 2022

Motivation

Protein functions are often described using the Gene Ontology (GO) which is an ontology consisting of over 50 000 classes and a large set of formal axioms. Predicting the functions of proteins is one of the key challenges in computational biology and a variety of machine learning methods have been developed for this purpose. However, these methods usually require a significant amount of training data and cannot make predictions for GO classes that have only few or no experimental annotations.

Results

We developed DeepGOZero, a machine learning model which improves predictions for functions with no or only a small number of annotations. To achieve this goal, we rely on a model-theoretic approach for learning ontology embeddings and combine it with neural networks for protein function prediction. DeepGOZero can exploit formal axioms in the GO to make zero-shot predictions, i.e., predict protein functions even if not a single protein in the training phase was associated with that function. Furthermore, the zero-shot prediction method employed by DeepGOZero is generic and can be applied whenever associations with ontology classes need to be predicted.

Availability and implementation

http://github.com/bio-ontology-research-group/deepgozero.

Supplementary information

Supplementary data are available at Bioinformatics online.
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information
Authors: Ahsan Faizy , Yan Zichao , Precup Doina , Blanchette Mathieu
Published: April 2022

Motivation

The computational prediction of regulatory function associated with a genomic sequence is of utter importance in -omics study, which facilitates our understanding of the underlying mechanisms underpinning the vast gene regulatory network. Prominent examples in this area include the binding prediction of transcription factors in DNA regulatory regions, and predicting RNA–protein interaction in the context of post-transcriptional gene expression. However, existing computational methods have suffered from high false-positive rates and have seldom used any evolutionary information, despite the vast amount of available orthologous data across multitudes of extant and ancestral genomes, which readily present an opportunity to improve the accuracy of existing computational methods.

Results

In this study, we present a novel probabilistic approach called PhyloPGM that leverages previously trained TFBS or RNA–RBP binding predictors by aggregating their predictions from various orthologous regions, in order to boost the overall prediction accuracy on human sequences. Throughout our experiments, PhyloPGM has shown significant improvement over baselines such as the sequence-based RNA–RBP binding predictor RNATracker and the sequence-based TFBS predictor that is known as FactorNet. PhyloPGM is simple in principle, easy to implement and yet, yields impressive results.

Availability and implementation

The PhyloPGM package is available at https://github.com/BlanchetteLab/PhyloPGM

Supplementary information

Supplementary data are available at Bioinformatics online.
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance
Authors: Qiu Yutong , Kingsford Carl
Published: April 2022

Motivation

Intra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets.

Results

We extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated T-cell receptor sequences and actual Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%.

Availability and implementation

Data and source code for reproducing the experiments are available at: https://github.com/Kingsford-Group/gtedemedtest/.

Supplementary information

Supplementary data are available at Bioinformatics online.
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data
Authors: Song Dongyuan , Xi Nan Miles , Li Jingyi Jessica , Wang Lin
Published: April 2022

The number of cells measured in single-cell transcriptomic data has grown fast in recent years. For such large-scale data, subsampling is a powerful and often necessary tool for exploratory data analysis. However, the easiest random subsampling is not ideal from the perspective of preserving rare cell types. Therefore, diversity-preserving subsampling is required for fast exploration of cell types in a large-scale dataset. Here, we propose scSampler, an algorithm for fast diversity-preserving subsampling of single-cell transcriptomic data.

Availability and implementation

scSampler is implemented in Python and is published under the MIT source license. It can be installed by “pip install scsampler” and used with the Scanpy pipline. The code is available on GitHub: https://github.com/SONGDONGYUAN1994/scsampler. An R interface is available at: https://github.com/SONGDONGYUAN1994/rscsampler.

Supplementary information

Supplementary data are available at Bioinformatics online.