bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of Race in Social and Emotional Learning (SEL) Training for Preservice School Social Workers and Teachers
Authors: Humphries Marisha L , McKay-Jackson Cassandra
Published: November 2021

Race is often ignored as a core component of social and emotional competency (SEC) and social and emotional learning (SEL). This study explored preservice school social worker and elementary teacher interns’ participation in a collaborative, multidisciplinary SEL training curriculum that integrates race. Nine preservice trainees (majority White women) participated in the collaborative training. Qualitative methodology was utilized to examine and access the training. Content analysis revealed three themes from a study of the interns’ participation in the training: function of color blindness, “I haven’t noticed,” and silencing of emotions. While interns acknowledged the importance of race, they were unclear on how students’ racial identities were a key component of students’ SEC. They also struggled to find ways to incorporate race in their implementation of SEL. Findings are discussed regarding the role of race and preservice training in SEL.
Accounting for GIA signal in GRACE products
Authors: Vishwakarma Bramha Dutt , Horwath Martin , Groh Andreas , Bamber Jonathan L
Published: November 2021

The Gravity Recovery and Climate Experiment (GRACE) observes gravitational potential anomalies that include the effects of present-day surface mass change (PDSMC)- and glacial isostatic adjustment (GIA)-driven solid Earth mass redistribution. Therefore, GIA estimates from a forward model are commonly removed from GRACE to estimate PDSMC. There are several GIA models and to facilitate users in using a GIA model of their choice, both GRACE and GIA products are made available in terms of global gridded fields representing mass anomaly. GRACE-observed gravitational potential anomalies are represented in terms of equivalent water height (EWH) with a relation that accounts for an elastic solid Earth deformation due to PDSMC. However, for obtaining GIA EWH fields from GIA gravitational potential fields, two relations are being used: one that is similar to that being used for GRACE EWH and the other that does not include an elastic deformation effect. This leaves users with the possibility of obtaining different values for PDSMC with a given GRACE and GIA field. In this paper, we discuss the impact of this problem on regional mass change estimates and highlight the need for consistent treatment of GIA signals in GRACE observations.
Effect of different selenium sources and concentrations on glutathione peroxidase activity and cholesterol metabolism of beef cattle
Authors: da Silva Janaina S , Rosa Alessandra F , Moncau Cristina T , Silva-Vignato Bárbara , Pugine Silvana Marina P , de Melo Mariza P , Sanchez João Marcelo D , Zanetti Marcus Antonio
Published: November 2021

The objective of this study was to investigate the effects of different Se sources and concentrations on glutathione forms and cholesterol metabolism in beef cattle. Sixty-three Nellore bulls (412 ± 19 kg body weight (BW); 24 mo old) were randomly assigned to a completely randomized design in a 2 × 3 + 1 factorial arrangement (63 pens; one animal/pen) with two Se sources (sodium selenite, ING and Se-yeast, ORG), three concentrations (0.3, 0.9, and 2.7 mg supplemental Se/kg dry matter (DM)), and control treatment (without Se supplementation) fed for 90 d. Blood samples were collected on day 0, 28, 56, and 84. Muscle and liver samples were collected at harvest. Hepatic GSSG (P = 0.004), GSH/GSSG ratio (P = 0.030), and GSH-Px (P = 0.004) were affected by Se source × concentration interaction. Oxidized glutathione was higher in the ORG group vs. ING at concentration 2.7 mg supplemental Se/kg DM, but at 0.3 mg supplemental Se/kg DM the ING group was higher than ORG. The liver GSH-Px activity was higher in the ORG group vs. ING at concentration 0.9 and 2.7 mg supplemental Se/kg DM. The GSH/GSSG ratio was the highest in animals fed 0.3 mg supplemental Se/kg DM of ORG. Selenium liver concentration increased linearly with the supplemental Se concentration in the diet (y = 0.0583 + 0.4254x, R2 = 0.92, P < 0.0001), regardless of source. Total meat cholesterol was greater (P < 0.001) in CON (control) vs. SUP (supplemented, regardless source) group. The muscle GSH-Px activity was higher (P < 0.001) in SUP vs. CON and increased (P < 0.004) with increasing supplemental Se concentrations. There was an increase on very low-density lipoprotein (VLDL), glucose, and triglycerides in ORG vs. ING (P ≤ 0.035). In general, serum Se was higher (P < 0.001) in SUP vs. CON and increased with increasing supplemental Se concentration. Lastly, the 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR) concentration was lower (P = 0.002) in SUP (0.39 ng/mL) vs. CON (0.55 ng/mL). Selenium supplementation with different sources and concentrations has the potential to affect cholesterol metabolism by affecting GSH/GSSG ratio, GSH-Px, and the HMGCR.
Impacts of polyclonal antibody preparations from avian origin as a feed additive to beef cattle: immune responses during the step-up transition diets
Authors: Silva Gleise M , Podversich Federico , Schulmeister Tessa M , Sanford Carla , Cangiano Lautaro R , Nelson Corwin D , DiLorenzo Nicolas
Published: November 2021

This study investigated the effects of feeding an avian-derived polyclonal antibody preparation (PAP; CAMAS, Inc.) against Streptococcus bovis, Fusobacterium necrophorum, and lipopolysaccharides (LPS; 40%, 35%, and 25% of the preparation, respectively) on immune responses (haptoglobin [Hp], serum amyloid A [SAA], rectal temperature [RT], leukocyte counts, and expression of cell adhesion molecules cluster of differentiation [CD] CD11b, CD14, and CD62L) of beef steers during a 21-d step-up adaptation to a high-grain diet. Eight ruminally cannulated Angus crossbred beef steers (658 ± 79 kg of BW) were assigned in a cross-over design and transitioned from a diet containing bermudagrass hay (Cynodon dactylon (L.) Pers.) ad libitum plus 0.45 kg/d of molasses with 0 (CON) or 3 g of PAP to a high-grain diet. Transition consisted of three 7-d steps of increased inclusion of cracked corn (35%, 60%, and 82% of the diet dry matter for STEP1, STEP2, and STEP3, respectively). On each transition day and 7 d after STEP3 (STEP3-7d), RT was obtained every 3 h for a total of 24 h, whereas blood was collected on days 0, 1, and 3, relative to diet transition. There were no effects of PAP inclusion in any of the blood parameters (P > 0.11). However, a tendency for day effect (P = 0.10) was observed for concentrations of Hp, which were greater on days 3 and 7 vs. day 0 relative to the second diet transition (STEP2). Plasma concentrations of SAA were greater on days 1, 3, and 7 compared to day 0 during STEP1 (P = 0.01), while during STEP2 and STEP3, SAA concentrations increased (P < 0.01) from day 0 to 3. During STEP2, PAP steers tended to have lower (P = 0.08) RT than CON steers. Neutrophil and monocyte counts were the least during STEP3 (P < 0.01), whereas expression of CD11b and CD62L was the least through forage feeding (P < 0.01). Concentration of starch in the diet was correlated to all the variables tested (P ≤ 0.01), except for the percentage of B cells (P = 0.22). Yet only ruminal pH, RT, monocyte, and neutrophil counts presented strong correlation coefficients. In conclusion, the step-up transition from forage to high-grain diets triggered systemic inflammation in beef steers as observed by increased plasma concentrations of Hp, SAA, and expression on adhesion molecules in leukocytes. However, feeding polyclonal antibody preparations against S. bovis, F. necrophorum, and LPS did not provide benefits to mitigate inflammation.
Comparison between methods for measuring fecal egg count and estimating genetic parameters for gastrointestinal parasite resistance traits in sheep
Authors: Boareki Mohammed N , Schenkel Flavio S , Willoughby Olivia , Suarez-Vega Aroa , Kennedy Delma , Cánovas Angela
Published: November 2021

Fecal egg count (FEC) is an indicative measurement for parasite infection in sheep. Different FEC methods may show inconsistent results. Not accounting for inconsistencies can be problematic when integrating measurements from different FEC methods for genetic evaluation. The objectives of this study were to evaluate the difference in means and variances between two fecal egg counting methods used in sheep—the Modified McMaster (LMMR) and the Triple Chamber McMaster (LTCM); to estimate variance components for the two FEC methods, treating them as two different traits; and to integrate FEC data from the two different methods and estimate genetic parameters for FEC and other gastrointestinal parasite resistance traits. Fecal samples were collected from a commercial Rideau-Arcott sheep farm in Ontario. Fecal egg counting was performed using both LMMR and the LTCM methods. Other parasite resistance trait records were collected from the same farm including eye score (FAMACHA), body condition score (BCS), and body weight (WT). The two FEC methods were highly genetically (0.94) and phenotypically (0.88) correlated. However, the mean and variance between the two FEC methods were significantly different (P < 0.0001). Therefore, re-scaling is required prior to integrating data from the different methods. For the multiple trait analysis, data from the two fecal egg counting methods were integrated (LFEC) by using records for the LMMR when available and replacing missing records with re-standardized LTCM records converted to the same mean and variance of LMMR. Heritability estimates were 0.12 ± 0.04, 0.07 ± 0.05, 0.17 ± 0.06, and 0.24 ± 0.07 for LFEC egg count, FAMACHA, BCS, and WT, respectively. The estimated genetic correlations between FEC and the other parasite resistance traits were low and not significant (P > 0.05) for FAMACHA (r = 0.24 ± 0.32) and WT (r = 0.22 ± 0.19), and essentially zero for BCS (r = −0.03 ± 0.25), suggesting little to no benefit of using such traits as indicators for LFEC.
The digital humanities and re-imagined language description: A linguistic model of Malay with potential for other languages
Authors: Don Zuraidah Mohd , Knowles Gerry
Published: November 2021

The declaration of 2019 as the International Year of Indigenous Languages raised the question how it will be possible in practice for hitherto uninvestigated languages to be investigated at all. The suggestion put forward in this article is that traditional language description reimagined in the context of the Digital Humanities has the capacity to create models, which can be re-used mutatis mutandis for other languages. The methodology makes use of MaLex, which is a collection of procedures and datasets designed for Malay in the first instance, but with the potential to be modified for other languages. MaLex is placed in its historical context within the Humanities, and digital procedures are explicitly connected to traditional scholarship. The use of digital methods creates new opportunities to scale up practical linguistic analysis using large datasets. MaLex procedures include a stemmer, a tagger, a parser, and a spelling-to-phoneme algorithm, and make a rough English translation of Malay text. MaLex simulates the approach of the practical linguist analysing a new language, and as new components are added, they are made to integrate with existing components, so that MaLex works like a single machine, drawing on an integrated infrastructure.
Atomic data calculations for Au i–Au iii and exploration in the application of collisional-radiative theory to laboratory and neutron star merger plasmas
Authors: McCann Michael , Bromley S , Loch S D , Ballance C P
Published: November 2021

Neutron binary star mergers have long been proposed as sufficiently neutron rich environments that could support the synthesis of rapid neutron capture elements (r-process elements) such as gold. However, the literature reveals that beyond neutral and singly ionized systems, there is an incompleteness of atomic data for the remaining ion stages of importance for mergers. In this work, we report on relativistic atomic structure calculations for Au i–Au iii using the grasp0 codes. Comparisons to calculations using the Flexible Atomic Code suggest uncertainties on average of 9.2 per cent, 5.7 per cent, and 3.8 per cent for Au i–Au iii level energies. Agreement around ∼50 per cent is achieved between our computed A-values and those in the literature, where available. Using the grasp0 structure of Au i, we calculated electron-impact excitation rate coefficients and use a collisional-radiative model to explore the excitation dynamics and line ratio diagnostics possible in neutron star merger environments. We find that proper accounting of metastable populations is critical for extracting useful information from ultraviolet–visible line ratio diagnostics of Au i. As a test of our data, we applied our electron-impact data to study a gold hollow cathode spectrum in the literature and diagnosed the plasma conditions as Te = 3.1 ± 1.2 eV and $n_\textrm {e} = 2.7^{+1.3}_{-0.9}\times 10^{13}$ cm−3.
BiPoS1 – a computer programme for the dynamical processing of the initial binary star population
Authors: Dabringhausen J , Marks M , Kroupa P
Published: November 2021

The first version of the Binary Population Synthesizer (BiPoS1) is made publicly available. It allows to efficiently calculate binary distribution functions after the dynamical processing of a realistic population of binary stars during the first few Myr in the hosting embedded star cluster. Instead of time-consuming N-body simulations, BiPoS1 uses the stellar dynamical operator $\Omega _{\rm dyn}^{\rho _{\rm ecl}}(\log _{10}(E_{\rm b}),t)$, which determines the fraction of surviving binaries depending on the binding energy of the binaries, Eb. The Ω-operator depends on the initial star cluster density, ρecl, as well as the time, t, until the residual gas of the star cluster is expelled. BiPoS1 has also a galactic-field mode, in order to synthesize the stellar population of a whole galaxy. At the time of gas expulsion, the dynamical processing of the binary population is assumed to efficiently end due to the subsequent expansion of the star cluster. While BiPoS1 has been used previously unpublished, here we demonstrate its use in the modelling of the binary populations in the Orion Nebula Cluster, in OB associations and as an input for simulations of globular clusters.
Leptomeningeal disease in neurosurgical brain metastases patients: A systematic review and meta-analysis
Authors: Tewarie Ishaan Ashwini , Jessurun Charissa A C , Hulsbergen Alexander F C , Smith Timothy R , Mekary Rania A , Broekman Marike L D
Published: November 2021

Background

Leptomeningeal disease (LMD) is a complication distinguished by progression of metastatic disease into the leptomeninges and subsequent spread via cerebrospinal fluid (CSF). Although treatments for LMD exist, it is considered fatal with a median survival of 2–4 months. A broader overview of the risk factors that increase the brain metastasis (BM) patient's risk of LMD is needed. This meta-analysis aimed to systematically review and quantitatively assess risk factors for LMD after surgical resection for BM.

Methods

A systematic literature search was performed on 7 May 2021. Pooled effect sizes were calculated using a random-effects model for variables reported by three or more studies.

Results

Among 503 studies, thirteen studies met the inclusion criteria with a total surgical sample size of 2105 patients, of which 386 patients developed LMD. The median incidence of LMD across included studies was 16.1%. Eighteen unique risk factors were reported as significantly associated with LMD occurrence, including but not limited to: larger tumor size, infratentorial BM location, proximity of BM to cerebrospinal fluid spaces, ventricle violation during surgery, subtotal or piecemeal resection, and postoperative stereotactic radiosurgery. Pooled results demonstrated that breast cancer as the primary tumor location (HR = 2.73, 95% CI: 2.12–3.52) and multiple BMs (HR = 1.37, 95% CI: 1.18–1.58) were significantly associated with a higher risk of LMD occurrence.

Conclusion

Breast cancer origin and multiple BMs increase the risk of LMD occurrence after neurosurgery. Several other risk factors which might play a role in LMD development were also identified.
Colour Doppler ultrasound and the giant cell arteritis probability score for the diagnosis of giant cell arteritis: a Canadian single-centre experience
Authors: Zarka Farah , Rhéaume Maxime , Belhocine Meriem , Goulet Michelle , Febrer Guillaume , Mansour Anne-Marie , Troyanov Yves , Starnino Tara , Meunier Rosalie-Sélène , Chagnon Isabelle , Routhier Nathalie , Bénard Valérie , Ducharme-Bénard Stéphanie , Ross Carolyn , Makhzoum Jean-Paul
Published: November 2021

Objectives

The aim was to compare the accuracy of colour Doppler ultrasonography (CDUS) and temporal artery biopsy (TAB) to establish the final diagnosis of GCA and to determine how the GCA probability score (GCAPS) performs as a risk stratification tool.

Methods

Descriptive statistics were performed on a retrospective cohort of patients referred to our vasculitis referral centre between 1 July 2017 and 1 October 2020 for suspected GCA. CDUS, TAB, centre-specific TAB (vasculitis centre vs referring hospitals) and GCAPS were compared against the final diagnosis of GCA as determined by a GCA expert; CDUS was also compared with TAB results.

Results

Data from 198 patients were included: 60 patients with GCA and 138 patients without GCA. Sixty-two patients had a TAB. Using the final diagnosis by a GCA expert as a reference, the sensitivity, specificity, positive predictive value and negative predictive value were 93.3%, 98.5%, 96.6% and 97.1% for CDUS and 69.2%, 100%, 100% and 81.8% for TAB, respectively. The false-negative rate was 6.7% for CDUS and 30.8% for TAB. False-negative TAB mostly occurred when performed in referring hospitals (57.1%) as opposed to our vasculitis centre (21.1%). With a cut-off at 9.5 points, sensitivity for GCAPS was 98.3% and specificity 74.3%.

Conclusion

CDUS of the temporal and axillary arteries showed a high sensitivity and specificity and helped to diagnose GCA in patients with negative TAB. We validated that GCAPS is a useful clinical tool, with a score of <9.5 making the diagnosis of GCA improbable.
Do Patients With Multiple Myeloma Enrolled in Clinical Trials Live Longer?
Authors: Aung Taing N. , Bickell Nina A. , Jagannath Sundar , Kamath Geetanjali , Meltzer Jeremy , Kunzel Brian , Egorova Natalia N.
Published: November 2021

Objectives:

Enrollment in clinical trials is thought to improve survival outcomes through the trial effect. In this retrospective observational cohort study, we aimed to discern differences in survival outcomes by clinical trial enrollment and race-ethnicity.

Materials and Methods:

Of 1285 patients receiving care for multiple myeloma at an National Cancer Institute designated cancer center from 2012 to 2018, 1065 (83%) were nontrial and 220 (17%) were trial participants. Time to event analyses were used to adjust for baseline characteristics and account for clinical trial enrollment as a time-varying covariate. We analyzed propensity-matched cohorts of trial and nontrial patients to reduce potential bias in observational data.

Results:

Trial patients were younger (mean age in years: 60 vs. 63; P<0.001), underwent more lines of therapy (treatment lines ≥6: 39% vs. 17%; P<0.001), and had more comorbidities than nontrial patients. After controlling for baseline characteristics and clinical trial enrollment as a time-varying covariate, no significant difference in survival was found between trial and nontrial participants (hazard ratio [HR]=1.34, 95% confidence intervals [CIs]: 0.90-1.99), or between propensity-matched trial and nontrial participants (205 patients in each cohort, HR=1.36, 95% CIs: 0.83-2.23). Subgroup analyses by lines of therapy confirmed results from overall analyses. We did not observe survival differences by race-ethnicity (Logrank P=0.09), though hazard of death was significantly increased for nontrial Black/Hispanic patients compared with trial White patients (HR=1.76, 95% CIs=1.01-3.08).

Conclusions:

This study did not find evidence of a significant survival benefit to trial enrollment among patients with multiple myeloma. Patients enrolled in clinical trials underwent more lines of therapy, suggesting they may have had more treatment-resistant cancers. A small survival benefit in this cohort may be obscured by the lack of difference in survival between trial and nontrial patients.
Reirradiation in Conservative Salvage of Recurrent Soft-tissue Sarcoma
Authors: Braschi Erica L. , Kharod Shivam M. , Morris Christopher G. , Spiguel Andre R. , Gibbs Charles P. , Scarborough Mark T. , Zlotecki Robert A.
Published: November 2021

Objective:

Compared with radical resection alone, perioperative radiation therapy (RT) combined with neurovascular preserving surgery is the standard for the management of virgin soft-tissue sarcomas. Yet, the optimal management of a local recurrence remains unclear. We report outcomes of patients with locally recurrent soft-tissue sarcoma treated with resection and reirradiation at the University of Florida.

Materials and Methods:

We reviewed the records of patients treated with primary conservative surgery and radiation for soft-tissue sarcoma followed by salvage resection and reirradiation for a local recurrence at our institution.

Results:

We analyzed 23 patients treated between 1976 and 2014 (median follow-up, 46 mo). Tumor sites included: proximal extremity, 11 patients; trunk, 6; distal extremity, 5; and head and neck, 1. All patients had conservative gross total resection of their recurrent tumor, without amputation. For reirradiation, 16 patients received external-beam RT alone, 6 received external-beam RT and brachytherapy, and 1 received brachytherapy alone. Two patients received chemotherapy. After retreatment, the 5-year overall survival, cause-specific survival, local control, and distant control rates were 39%, 42%, 46%, and 60%, respectively. Ten patients experienced local recurrences, 1 experienced regional recurrence, and 9 developed distant metastases. Retreatment-related complications ranged from delayed wound healing to limb amputation; 8 patients required amputation. Only 3 patients remained disease-free at last follow-up. No statistically significant associations were found between treatment factors (eg, RT dose) and local control.

Conclusions:

Achieving local control of recurrent soft-tissue sarcoma is challenging. Treatment with reoperation and reirradiation can lead to debilitating complications affecting function and quality of life.
Reported Clinical and Financial Performance of Hospitals With Physician CEOs Compared to Those With Nonphysician CEOs
Authors: Moores Leon E. , Landry Amy , Hernandez S. Robert , Szychowski Jeff M. , Borkowski Nancy
Published: November 2021

EXECUTIVE SUMMARY

Little work has been done comparing the performance of hospitals with physician CEOs versus nonphysician CEOs, despite the ease of identifying this characteristic and extant leadership theories suggesting a relationship between technical expertise and success in leading highly technical organizations. We performed a detailed analysis of several widely accepted measures of clinical and financial performance across a randomly selected group of U.S. acute care hospitals with more than 40 beds and found no statistically significant differences between the two groups. The 30-day acute myocardial infarction mortality rate showed a positive statistically significant difference in the bivariate analysis (p < .001), but the effect was nullified in the multivariable regression analysis.
Intraoperative Fluorescence With Second Window Indocyanine Green Enhances Visualization During Vestibular Schwannoma Surgery
Authors: Peng Kevin A. , Lekovic Gregory P.
Published: November 2021

Objective:

To investigate the utility of the so-called “second window” of indocyanine green (ICG) as a near-infrared fluorescent dye for intraoperative visualization.

Patients:

Three patients who underwent surgical resection of vestibular schwannoma (two retrosigmoid and one middle fossa approach).

Intervention(s):

Patients underwent intravenous infusion of ICG at a mean dose of 4.8 mg/kg at a mean of 15.3 hours before surgical incision. Once tumor dissection began, near-infrared fluorescence was used alongside conventional operative microscopy to visualize tumor tissue.

Main Outcome Measure(s):

Ability to distinguish tumor tissue from adjacent nerves.

Results:

Intraoperative fluorescence allowed for enhanced visualization of the tumor-nerve plane in all patients. However, the effect varied among patients, and the effect faded with increasing surgical time.

Conclusions:

ICG, a well-tolerated cyanine dye, demonstrates late fluorescence hours after administration secondary to diffusion into tumor as well as normal tissues (the so-called “second window” of fluorescence). Its fluorescence in the near-infrared spectrum is a promising adjunct for enhancing visualization of tumor planes during vestibular schwannoma surgery.
Brief Report: Rebound HIV Viremia With Meningoencephalitis After Antiretroviral Therapy Interruption After Allogeneic Bone Marrow Transplant
Authors: Capoferri Adam A. , Redd Andrew D. , Gocke Christopher D. , Clark Laura R. , Quinn Thomas C. , Ambinder Richard F. , Durand Christine M.
Published: November 2021

Background:

Allogeneic bone marrow transplant (alloBMT) in people living with HIV can lead to the undetectable levels of HIV reservoirs in blood, even using highly sensitive assays. However, with antiretroviral therapy (ART) interruption, rebound of HIV viremia occurs. The source of this rebound viremia is of interest in HIV cure strategies.

Methods:

Within a trial of alloBMT in individuals with hematologic malignancies and HIV (ClinicalTrials.gov, NCT01836068), one recipient self-interrupted ART after achieving >99.5% host cell replacement in peripheral blood by day 147 and developed severe acute retroviral syndrome with meningoencephalitis at 156 days post alloBMT. We isolated replication-competent HIV using a quantitative viral outgrowth assay at 100 and 25 days before alloBMT and from the same time points before alloBMT for HIV DNA and cell-associated RNA from peripheral blood mononuclear cells and resting memory CD4+ T cells. We isolated HIV RNA in plasma and cerebrospinal fluid (CSF) at viral rebound. We sequenced the RT-region of pol and performed neighbor-joining phylogenetic reconstruction.

Results:

Phylogenetic analysis revealed an identical viral sequence at both pre-alloBMT time points accounting for 9 of 34 sequences (26%) of the sampled HIV reservoir. This sequence population grouped with viral rebound sequences from plasma and CSF with high sequence homology.

Discussion:

Despite >99.5% replacement of host cells in peripheral blood, ART interruption led to HIV viral rebound in plasma and CSF. Furthermore, the rebound virus matched replication-competent virus from resting memory CD4+ T cells before alloBMT. This case underscores that HIV-infected recipient cells can persist after alloBMT and that latent replication-competent virus can reestablish infection.
The impact of COVID-19 on the worldwide air transportation network
Authors: Bao Xiaoge , Ji Peng , Lin Wei , Perc Matjaž , Kurths Jürgen
Published: November 2021

Air travel has been one of the hardest hit industries of COVID-19, with many flight cancellations and airport closures as a consequence. By analysing structural characteristics of the Official Aviation Guide flight data, we show that this resulted in an increased average distance between airports, and in an increased number of long-range routes. Based on our study of network robustness, we uncover that this disruption is consistent with the impact of a mixture of targeted and random global attack on the worldwide air transportation network. By considering the individual functional evolution of airports, we identify anomalous airports with high centrality but low degree, which further enables us to reveal the underlying transitions among airport-specific representations in terms of both geographical and geopolitical factors. During the evolution of the air transportation network, we also observe how the network attempted to cope by shifting centralities between different airports around the world. Since these shifts are not aligned with optimal strategies for minimizing delays and disconnects, we conclude that they are consistent with politics trumping science from the viewpoint of epidemic containment and transport.
Diurnal fluctuations in musical preference
Authors: Heggli Ole Adrian , Stupacher Jan , Vuust Peter
Published: November 2021

The rhythm of human life is governed by diurnal cycles, as a result of endogenous circadian processes evolved to maximize biological fitness. Even complex aspects of daily life, such as affective states, exhibit systematic diurnal patterns which in turn influence behaviour. As a result, previous research has identified population-level diurnal patterns in affective preference for music. By analysing audio features from over two billion music streaming events on Spotify, we find that the music people listen to divides into five distinct time blocks corresponding to morning, afternoon, evening, night and late night/early morning. By integrating an artificial neural network with Spotify's API, we show a general awareness of diurnal preference in playlists, which is not present to the same extent for individual tracks. Our results demonstrate how music intertwines with our daily lives and highlight how even something as individual as musical preference is influenced by underlying diurnal patterns.
Redox-mediated carbon monoxide release from a manganese carbonyl—implications for physiological CO delivery by CO releasing moieties
Authors: Barrett Jacob A. , Li Zhi , Garcia John V. , Wein Emily , Zheng Dongyun , Hunt Camden , Ngo Loc , Sepunaru Lior , Iretskii Alexei V. , Ford Peter C.
Published: November 2021

The dynamics of hydrogen peroxide reactions with metal carbonyls have received little attention. Given reports that therapeutic levels of carbon monoxide are released in hypoxic tumour cells upon manganese carbonyls reactions with endogenous H
2
O
2
, it is critical to assess the underlying CO release mechanism(s). In this context, a quantitative mechanistic investigation of the H
2
O
2
oxidation of the water-soluble model complex
fac
-[Mn(CO)
3
(Br)(bpCO
2
)]
2–
, (
A
, bpCO
2
2–
= 2,2′-bipyridine-4,4′-dicarboxylate dianion) was undertaken under physiologically relevant conditions. Characterizing such pathways is essential to evaluating the viability of redox-mediated CO release as an anti-cancer strategy. The present experimental studies demonstrate that approximately 2.5 equivalents of CO are released upon H
2
O
2
oxidation of
A
via pH-dependent kinetics that are first-order both in [
A
] and in [H
2
O
2
]. Density functional calculations were used to evaluate the key intermediates in the proposed reaction mechanisms. These pathways are discussed in terms of their relevance to physiological CO delivery by carbon monoxide releasing moieties.
Impairment effect of infantile coloration on face discrimination in chimpanzees
Authors: Kawaguchi Yuri , Nakamura Koyo , Tomonaga Masaki , Adachi Ikuma
Published: November 2021

Impaired face recognition for certain face categories, such as faces of other species or other age class faces, is known in both humans and non-human primates. A previous study found that it is more difficult for chimpanzees to differentiate infant faces than adult faces. Infant faces of chimpanzees differ from adult faces in shape and colour, but the latter is especially a salient cue for chimpanzees. Therefore, impaired face differentiation of infant faces may be due to a specific colour. In the present study, we investigated which feature of infant faces has a greater effect on face identification difficulty. Adult chimpanzees were tested using a matching-to-sample task with four types of face stimuli whose shape and colour were manipulated as either infant or adult one independently. Chimpanzees' discrimination performance decreased as they matched faces with infant coloration, regardless of the shape. This study is the first to demonstrate the impairment effect of infantile coloration on face recognition in non-human primates, suggesting that the face recognition strategies of humans and chimpanzees overlap as both species show proficient face recognition for certain face colours.
Transcriptome analysis of SARS-CoV-2 naïve and recovered individuals vaccinated with inactivated vaccine
Authors: Zhang Yuwei , Guo Xingyu , Li Cunbao , Kou Zengqiang , Lin Lanfang , Yao Mingxiao , Pang Bo , Zhang Xiaomei , Duan Qing , Tian Xueying , Xing Yufang , Jiang Xiaolin
Published: November 2021

The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naïve individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the host’s molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.
Monaural and binaural masking release with speech-like stimuli
Authors: Kim Hyojin , Ratkute Viktorija , Epp Bastian
Published: November 2021

The relevance of masking release by comodulation and interaural phase difference (IPD) for speech perception is still unclear. We used speech-like stimuli to link spectro-temporal properties of formants with masking release. The stimuli comprised a tone and three masker bands centered at formant frequencies F1, F2, and F3 derived from a consonant-vowel (/gu/, /fu/, and /pu/). The target was a diotic or dichotic frequency-modulated tone following F2 trajectories. Results showed no statistically significant comodulation masking release (CMR), while the binaural masking level difference (BMLD) was comparable to previous findings. The data suggest that factors other than comodulation may play a dominant role in grouping frequency components in speech.
Cellular and Synaptic Diversity of Layer 2-3 Pyramidal Neurons in Human Individuals
Authors: Planert Henrike , Mittermaier Franz Xaver , Grosser Sabine , Fidzinski Pawel , Schneider Ulf Christoph , Radbruch Helena , Onken Julia , Holtkamp Martin , Schmitz Dietmar , Alle Henrik , Vida Imre , Geiger Jörg Rolf Paul , Peng Yangfan
Published: November 2021

Understanding the functional principles of the human brain requires deep insight into the neuronal and network physiology. To what extent such principles of cellular physiology and synaptic interactions are common across different human individuals is unknown. We characterized the physiology of ~1200 pyramidal neurons and ~1400 monosynaptic connections using advanced multineuron patch-clamp recordings in slices from human temporal cortex. To disentangle within and between individual sources of heterogeneity, we recorded up to 100 neurons per single subject. We found that neuronal, but not synaptic physiology varied with laminar depth. Connection probability was ~15% throughout layer 2-3. Synaptic amplitudes exhibited heavy-tailed distributions with an inverse power law relationship to short term plasticity. Neurons could be classified into four functional subtypes. These general principles of microcircuit physiology were common across individuals. Our study advances the understanding of human neuron and synaptic diversity from an individual and phenotypic perspective.
Posterior integration and thalamo-frontotemporal broadcasting are impaired in disorders of consciousness
Authors: Panda Rajanikant , López-González Ane , Gilson Matthieu , Gosseries Olivia , Thibaut Aurore , Frasso Gianluca , Cecconi Benedetta , Escrichs Anira , Deco Gustavo , Laureys Steven , Zamora-López Gorka , Annen Jitka
Published: November 2021

The study of the brain’s static and dynamical activity is opening a valuable source of assistance for the clinical assessment of patients with disorders of consciousness. For example, glucose uptake and dysfunctional spread of naturalistic and synthetic stimuli has proven useful to characterize hampered consciousness. However, understanding of the mechanisms behind loss of consciousness following brain injury is still missing. Here, we study the propagation of endogenous and in-silico exogenous perturbations in patients with disorders of consciousness, based upon directed and causal interactions estimated from resting-state fMRI. We found that patients with disorders of consciousness suffer decreased capacity for neural propagation and responsiveness to events, and that this can be related to glucose metabolism as measured with [18F]FDG-PET. In particular, we show that loss of consciousness is related to the malfunctioning of two neural circuits: the posterior cortical regions failing to convey information, in conjunction with reduced broadcasting of information from subcortical, temporal, parietal and frontal regions. These results seed light on the mechanisms behind disorders of consciousness, triangulating network function with basic measures of brain integrity and behavior.

Highlights

Propagation of neural events and network responses are disrupted in patients with DoC.

Loss of consciousness is related to the malfunctioning of two neural circuits.

Posterior cortical regions lack to integrate information in altered consciousness.

Breakdown of information broadcasting of subcortical cortical areas in DoC.

Loss of network responses in DoC patients is related to glucose metabolism.
Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese Subpopulations
Authors: Zou Xing , He Guanglin , Liu Jing , Jiang Lirong , Wang Mengge , Chen Pengyu , Hou Yiping , Wang Zheng
Published: November 2021

Genetic findings suggested that ethnolinguistically diverse populations in China harbor differentiated genetic structure and complex evolutionary admixture history, which provide the genetic basis and theoretical foundation for forensic biogeographical ancestry inference (BGAI). Forensic assays for BGAI among intracontinental eastern Eurasians were previously conducted mainly based on the SNPs or InDels. Microhaplotypes, as a set of closely linked SNPs within 200 base pairs, possess the advantages of both STR and SNP and have great potential in forensic ancestry inference. However, the developed forensic assay based on the ancestry informative microhaplotypes in the BGAI remained to be comprehensively explored, especially in China with enriching genetic diversity. Here, we described a new BGAI panel based on 21 novel identified ancestry informative microhaplotypes that focused on dissected finer-scale ancestry composition of Chinese populations. We initially screened all possible microhaplotypes with high Fstvalues among five East Asian populations and finally employed 21 candidate microhaplotypes in two multiplex SNaPshot assays. Forensic amplification efficiency and statistically/physically phased haplotypes of the 21 microhaplotypes were validated using both SNaPshot and massively parallel sequencing (MPS) platforms. Followingly, we validated the efficiency of these microhaplotypes for BGAI in 764 individuals from ten Chinese populations. Fine-scale ancestry source and ancestry proportion estimated by the principal component analysis (PCA), multidimensional scaling (MDS), phylogenetic tree and model-based STRUCTURE among worldwide populations and East Asians showed that our customized panel could provide a higher discrimination resolution in both continental population stratification and East Asian regional substructure. East Asian populations could be further classified into linguistically/geographically different intracontinental subpopulations (Tibeto-Burman, Tai-Kadai and others). Finally, we obtained a higher estimated accuracy using training and tested datasets in the microhaplotype-based panel than traditional SNP-based panels. Generally, the above results demonstrated that this microhaplotype panel was robust and suitable for forensic BGAI in Chinese populations, which not only provided a high discriminatory power for continental populations but also discriminated East Asians into linguistically restricted subpopulations.
Prospects of telomere-to-telomere assembly in barley: analysis of sequence gaps in the MorexV3 reference genome
Authors: Navrátilová Pavla , Toegelová Helena , Tulpová Zuzana , Kuo Yi-Tzu , Stein Nils , Doležel Jaroslav , Houben Andreas , Šimková Hana , Mascher Martin
Published: November 2021

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, i.e. a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyze sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.
Cerebral perfusion imaging: Hypoxia-induced deoxyhemoglobin or gadolinium?
Authors: Sayin E.S , Schulman J. , Poublanc J. , Levine H. , Venkatraghavan L. , Uludag K. , Duffin J. , Fisher J.A. , Mikulis D.J. , Sobczyk O.
Published: November 2021

Assessment of resting cerebrovascular perfusion measures (mean transit time, cerebral blood flow and cerebral blood volume) with magnetic resonance imaging currently requires the intravascular injection of the dynamic susceptibility contrast agent gadolinium. An initial comparison between hypoxia-induced deoxyhemoglobin and gadolinium was made for these measures in six healthy participants. A bolus of deoxyhemoglobin is generated in the lung via transient hypoxia induced by an available computer-controlled gas blender technology employing sequential gas delivery (RespirAct™). We hypothesised and confirmed perfusion measures from both susceptibility contrast agents would yield similar spatial patterns of cerebrovascular perfusion measures. We conclude that hypoxia-induced deoxyhemoglobin, an endogenously, non-invasively generated, non-allergenic, non-toxic, recyclable, environmentally innocuous molecule, may be suitable to become the first new magnetic resonance imaging susceptibility contrast agent introduction since gadolinium.
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks
Authors: Wang Yuge , Liu Tianyu , Zhao Hongyu
Published: November 2021

Motivation

With the advancement of technology, we can generate and access large-scale, high dimensional and diverse genomics data, especially through single-cell RNA sequencing (scRNA-seq). However, integrative downstream analysis from multiple scRNA-seq datasets remains challenging due to batch effects.

Results

In this paper, we propose a light-structured deep learning framework called ResPAN for scRNA-seq data integration. ResPAN is based on Wasserstein Generative Adversarial Network (WGAN) combined with random walk mutual nearest neighbor pairing and fully skip-connected autoencoders to reduce the differences among batches. We also discuss the limitations of existing methods and demonstrate the advantages of our model over seven other methods through extensive benchmarking studies on both simulated data under various scenarios and real datasets across different scales. Our model achieves leading performance on both batch correction and biological information conservation and maintains scalable to datasets with over half a million cells.

Availability

An open-source implementation of ResPAN and scripts to reproduce the results can be downloaded from:https://github.com/AprilYuge/ResPAN.

Contact

hongyu.zhao@yale.edu
A Computational Modeling Framework to Analyze Synovial-Tissue Based Drug Targets and Diagnostic Biomarkers in Rheumatoid Arthritis
Authors: Latawa Paridhi , Chrisman Brianna
Published: November 2021

Rheumatoid Arthritis (RA) is an inflammatory autoimmune disease that affects 23 million people worldwide. It is a clinically heterogeneous disorder characterized by the attack of inflammatory chemicals on the synovial tissue that lines joints. It is advantageous to develop effective, targeted treatments and identify specific diagnostic biomarkers for RA before extensive joint degradation, bone erosion, and cartilage destruction. Current modes of RA treatments have alleviated and notably halted the progression of RA. Despite this, not many patients reach low disease activity status after treatment, and a significant number of patients fail to respond to medication due to drug non-specificity. While the reasons for these rates remain unknown, the cellular and molecular signatures present in the synovial tissue for RA patients likely play a role in the varied treatment response. Thus, a drug that particularly targets specific genes and networks may have a significant effect in halting the progression of RA. This study evaluates and proposes potential drug targets through in silico mathematical modeling of various pathways of interest in RA. To understand how drugs interact with genes, we built a mathematical model with 30 two-gene and three-gene network interactions and analyzed the effect of 92 different perturbations to rate constants. We determined that inhibition of the LCK-CD4, VAV1-CD4, and MLT-ROR pathways could potentially serve as drug targets. We also found that increased activity of the DEC2-IL1β and the NF-kB-interleukin pathway and the decreased activity of the TNF-α-REV-ERB pathway could serve as diagnostic biomarkers.