bluuebunny/crossref_metadata_2025 huggingface dataset:
PSIX-24 Genome-wide association mapping for additive and dominance effects in pig fertility
Authors: Bakoev Siroj , Getmantseva Lyubov , Bakoev Faridun , Shevtsova Varvara , Kostyunina Olga V , Getmantseva Varvara , Bakoev Nekruz , Kolosov Anatoly , Usatov Alexander
Published: October 2021

The aim of the work was to conduct GWAS for Total Number Born (TNB) based on the Gradient Boosting Machine (GBM) algorithm, taking into account additive and dominance effects. The study population consisted of 218 Landrace sows. DNA samples were genotyped using GGP HD Porcine. After filtering, 40358 SNPs are left for further analysis. The target variable is the Total Number Born estimated from the third farrow. To assess the additive (model A) and dominant (model D), the coding 0/1/2 and 0/1/0 were used, respectively. Based on the test results, the top 50 SNPs were selected for each of the models in accordance with the relative importance. Of the top 50 SNPs determined by model D, 36 SNPs were identified based on model A (of which 14 SNPs were included in the top of model A). However, the top 14 SNPs for Model D showed relative importance = 0 for Model A. The genes identified in Models A and D are responsible for Molecular functions: binding (GO: 0005488), catalytic activity (GO: 0003824), and transcriptional regulator activity (GO: 0140110); Biological process: cellular process (GO: 0009987), biological regulation (GO: 0065007), metabolic process (GO: 0008152); Cellular component: part of a cell (GO: 0044464) and a cell (GO: 0005623). Further research will allow a more detailed study of the genetic electrical energy of fertility traits in pigs. The results showed that the dominance effects has additional value for genomic effects that control pig fertility. This research was performed with financial support from the Russian Science Foundation (RSF) 19-76-10012.
PSII-B-24 Use of the Elnady technique of tissue preservation to preserve specimens for use in undergraduate animal science courses
Authors: Daniel Jay A , Kukor Isabella
Published: October 2021

The use of tissue specimens for undergraduate instruction is a very valuable tool. However, fresh tissue specimens are not always available and many common preservation techniques can result in discoloration, offensive odors, and/or dangerous chemical residues. The Elnady Technique was developed as a means to produce tissue specimens that “are realistic, durable, have no offensive odor, and are dry, soft and flexible” (Elnady, F.A. 2016 The Elnady Technique: An innovative, new method for tissue preservation. Altex. 33:237–242. doi:10.14573/altex.1511091). Briefly for soft tissue, specimens were preserved by fixing in formalin for one week. The tissue specimen was then dehydrated with a series of acetone baths changed weekly. Once the tissue was fully dehydrated, the specimen was impregnated in glycerin by full immersion in a glycerin bath for one to two weeks. Excess glycerin was then removed by draining followed by immersion in cornstarch for one to two weeks. Cornstarch residue was removed with a soft brush, and the specimen was stored in a plastic bag. Multiple specimens (including female reproductive tract of the cat, goat, horse, and sow; digestive tract of barred owl, cat, chicken, and dog; one day old lamb stomach; goat rumen, reticulum, omasum, and abomasum; deer testicle; and sheep heart and kidney) have been preserved and used in various animal science course laboratories (75 laboratory sections and over 1000 students at Berry College). Some of the specimens have been in use for five years and are still in usable condition. The Elnady Technique has proven to be a useful means of preserving tissue samples used in undergraduate animal science courses.
Disaster Prevention Achieved
Authors: McLean Andrew J. , Schwert Donald P. , Macek-Rowland Kathleen M. , DeSutter Thomas M. , O'Neill H. Katherine , Shultz James M.
Published: October 2021

Many communities in the US Upper Midwest have been battling record floods in recent decades. This chapter focuses on a spring flood event in 2009, when the Greater Fargo area avoided destruction from the Red River of the North by utilizing mitigation efforts. Included in the undertaking was the mobilization of the community to place millions of sandbags, as well as the creative repurposing of resources. This case study presents a model of community resilience in a geographically vulnerable region. It illustrates the achievement of flood disaster prevention in the face of imminent and severe threat; the reinforcement and enhancement of community resilience based on averting disaster; the channeling of fear-related behaviors into constructive community actions; and the complexity of factors that create unique flood risks along the Red River of the North. Lessons-learned provided for not only a recovery framework, but also a recognition of the value of behavioral health leadership in disaster situations.
Sleeping to Dream, Develop, and Resist Decline
Authors: Hughes Katharine , Khosla Payal , Pisani Lauren , Spanò Goffredina , Edgin Jamie O.
Published: October 2021

Sleep quality is increasingly recognized as a potential factor influencing healthy cognitive and neural development across the lifespan. It is becoming more recognized as an important factor for persons with Down syndrome, and this chapter describes the most recent literature regarding sleep disturbance, its correlates, and findings from animal models in this population. The authors discuss the relation of poor sleep to behavioral, brain, and cognitive dysfunction and highlight the family consequences for altered sleep in children with Down syndrome. These pervasive sleep deficits have the potential to derail cognitive development during critical periods for language learning and could also exacerbate age-related cognitive decline. The authors hope that this compilation of evidence regarding sleep deficits in persons with Down syndrome will help facilitate more treatment studies for sleep disorders in this population, including treatments aimed at poor sleep in infants, as well as mid-adulthood, which may lessen or delay the impact of the pathological progression of Alzheimer’s disease. Methodological challenges to sleep research are discussed, and future directions for this field are highlighted.
Lévi-Strauss’s Critique of Durkheim
Authors: Xie Jing
Published: October 2021

Lévi-Strauss’s critique of Durkheim is considered an important one for two reasons. First, it is a discussion about the nature of social reality, and it therefore raises questions about the philosophical foundations of Durkheimian sociology. Second, it is regarded as a turning point in the French tradition of social anthropology, Lévi-Strauss’s purpose being to put forward structuralism as a solution to Durkheimian difficulties. In this chapter, first I outline Lévi-Strauss’s core arguments, and then I reassess the significance of his critique in light of the recent debates about his structuralist program in France. I will show that the orthodox view on the relation between the Durkheim school and Lévi-Strauss’s structuralism is oversimplified because it relies heavily on Lévi-Strauss’s own claims, and as a consequence, also oversimplifies Durkheim’s account of social reality. By examining concepts such as “symbolism,” “obligation,” “institution,” “norm,” and “action” in both Durkheim’s and Lévi-Strauss’s theory, I will show that Lévi-Strauss’s structuralist turn is in fact a cognitivist one, which, instead of offering solutions to Durkheimian questions, dismisses those questions.
What The Slants’ First Amendment Case at the Supreme Court Actually Won
Authors: Tam Simon
Published: October 2021

This is a first-person account of the First Amendment case that rocked the nation. Much has been written about The Slants’ trademark case, which was decided at the Supreme Court, from NPR to Rolling Stone, but nearly everything published focused on the Washington Football team’s name and fear about a floodgate of hate speech. This article provides the argument for freedom of expression using an equity lens, moving it from abstract legal theory to a personal account of what the legal system and its procedures are actually like for those who wish to create social change.
The Music Modernization Act
Authors: Gorgoni Adam
Published: October 2021

This chapter is a songwriter’s essay on the Music Modernization Act and how it attempts to address the future of the songwriting profession in the digital age. Although the advent of streaming has resuscitated the music industry writ large, songwriters—unlike artists and record labels—are regulated by the government in ways that have stopped them from receiving their fair share of the growing pie. The author explains from a songwriter’s perspective how the MMA was designed to address these issues and assesses its strengths and weaknesses, the compromises that led to its passage, and the challenges going forward.
Green Industrial Policy in Comparative Perspective
Authors: Lewis Joanna I.
Published: October 2021

The deployment of renewable energy (RE) is increasing around the world, driven in part by the global climate commitments that have been adopted by almost 200 countries under the Paris Agreement. It is therefore important to understand how countries are adopting national strategies to promote green growth through RE development and, in particular, the role of “green industrial policies.” Industrial policies include a variety of protectionist measures that encourage domestic manufacturing for RE and raise barriers to foreign entry into domestic markets, setting up an inherent tension between low-carbon development and international trade. This chapter reviews the policies and incentives commonly used to support RE deployment as well as the localization of RE manufacturing. It then turns to a review of the green industrial policy strategies of the Chinese wind sector and the Indian solar sector—two examples of using green industrial policy with different outcomes. While green industrial policy helps states justify the low-carbon transition, it also potentially makes that transition costlier and more inefficient. The chapter ends with recommendations for ongoing policy discussions including the need for continued engagement about how to best foster clean energy innovation, rapid technology deployment, and economic development with a shared vision that does not leave emerging and developing countries behind.
Introduction
Authors: Pevehouse Jon C. W. , Seabrooke Leonard
Published: October 2021

This introductory chapter provides an overview of the evolution of international political economy (IPE) scholarship while laying out some of the themes that are discussed across the chapters in this book. IPE was born out of a recognition that politics mattered for economics and vice-versa, and as a practical, problem-oriented field. It continues to be so today, even if there appear to be theoretical and methodological camps engaging in differing research programs. The chapter then considers some of the commonalities among IPE scholars. Ultimately, challenges confronted by peoples, states, and firms lie at the center of research in IPE. While individual scholars make different choices as to the theoretical tools they use to understand and analyze those problems, and that there may be patterns to those choices, all of this is in the service of improving knowledge about the interactions that form the international political economy.
Nationalism and Politics in Zimbabwe
Authors: Mlambo Alois S.
Published: October 2021

This chapter focuses on nationalism in past and present Zimbabwean politics. It first traces the history and nature of anti-colonial nationalism in Zimbabwe, after which it sets out continuities and discontinuities of anti-colonial nationalism in independent Zimbabwe. The chapter is principally interested in the post-2000 years, which witnessed the rise of a particular and influential authoritarian nationalism and its temporary decline in the period November 2017 to August 2018. The chapter maintains that after 2000, the governing Zimbabwe African National Union–Patriotic Front (ZANU–PF) party propagated an exceedingly parochial and divisive authoritarian nationalism, predicated on loyalty to the ruling party. This authoritarian nationalism was prompted by the entrance of a credible opposition challenger to ZANU–PF in elections and was undergirded by a discriminatory rendition of Zimbabwe’s independence struggle history. ZANU–PF’s authoritarian nationalism was hardly brand new, since it had long roots in Zimbabwe’s anti-colonial nationalism, but its vigour and methodical promulgation by ZANU–PF constituted substantial discrepancies with past variations. Finally, the chapter argues that the removal of long-time ZANU–PF leader Robert Mugabe in a military coup in 2017 resulted in only a brief hiatus in ZANU–PF’s authoritarian nationalism, underscoring the deeply embedded nature of the ruling party’s authoritarian nationalist politics.
Vigilantism and Security-Making
Authors: Burrell Jennifer
Published: October 2021

Vigilantism and security-making ask that we both acknowledge the importance of legal pluralism (and its lived, and often contradictory, experiences), and that we recognize its limits. They insist that we acknowledge statecraft as a process engaged in by state and non-state actors, and that we rethink the contours of the contemporary state and the role of law within it. In imagining how anthropologists, lawyers, and legal scholars might think through these issues collaboratively and productively, this chapter suggests that legal pluralism can only take us so far. Ethnography is crucial to understanding how people engage, often simultaneously, various domains of law and how those domains themselves are also objects for scrutiny and investigation. Bringing these insights to policymaking and legal reform across various emerging fields, I suggest that vigilantism asks us to think about violence and to examine the roles and receptions of security-making and their integration into legal domains.
Greek Sanctuaries and Stadia
Authors: Romano David Gilman
Published: October 2021

The stadium (stadion) included the racecourse proper (dromos; of 600 feet) and the spectator area. Originally using natural slopes for onlookers, the stadia became more elaborate, with stone seating and complex starting lines (husplyges), in the Hellenistic and Roman periods. The second-century-bce stadium-cum-theatre at Pergamon is of special note, resembling in concept the fourth-century-bce structure on the Pnyx in Athens. Other stadia surveyed here are at Messene (Peloponnese) and Aphrodisias (Caria). Water channels allowed the track to be watered to avoid hardening. A 100-foot-square (plethron) space was used for field events. Most stadia had formal entrances, some using vaulted ‘tunnels’ (Olympia, Nemea, Delphi, and Epidauros). The history of certain stadia is traced: Olympia, Corinth, Halieis, Mt Lykaion (a hippodrome-cum-stadium), Rome (stadium of Domitian), Isthmia, Nemea, Delphi, and facilities at some civic and rural sanctuaries.
Sport and Spectacle in the Greek Bronze Age
Authors: Younger John G.
Published: October 2021

e (including bull-catching, bull-leaping, and bull-sacrifice), Minoan and Mycenaean frescoes, vase paintings, and stone relief vases depict boxing and wrestling, and competitions with special clothing, protective gloves, and physical restraints or handicaps. Less well known are the depictions of archers, foot-racers, and acrobats. Competition may arguably include artistic representations of game boards and gaming, dance performances, and processions, and descriptions of poetry and musical contests in Homer and Hesiod and of discus throwing in mythology. There is also architectural evidence for enclosing the central courts in the Minoan palaces for protection and seating of spectators. Depictions on eighth-century-bce pottery testify to chariot-racing, musical performances, horsemanship, and the hunt. We also consider passim the participation of women in sport and competition, drawing upon Aegean Bronze Age representations of women archers, hunters, and charioteers, and upon classical mythology for their participation in early foot-races, wrestling, and the hunt.
Greek Hippic Contests
Authors: Nicholson Nigel
Published: October 2021

Hippic contests constituted a surprisingly complex and contested semiotic system. This essay examines the hierarchies that structured this system to show how hippic contests gave visible form to various values and hierarchies that underpinned the larger social order. Equestrian contests as a whole were privileged over gymnastic contests; certain equestrian events were privileged over others (chariot over horse, four-horse over two-horse, stallion over mare, horse over mule); and the owner and the horse were privileged over the driver. In each case, however, it is also possible to trace challenges to these hierarchies, so that hippic contests should be thought of not so much as a vehicle for affirming a certain social order than as a particularly visible locus of ideological struggle.
Introduction
Authors: Novenson Matthew V.
Published: October 2021

‘Reading Paul’ is not, and never has been, just one thing. It has always been a matter of the particular questions and interests that the reader brings to the corpus of ancient texts written by, about, or in the name of the apostle. En route to this conclusion, this introduction kicks off the volume by performing several essential tasks. It offers a justification for the contents of the volume, explaining what is meant by the label ‘Pauline studies’ and exploring why it constitutes a (sub-)field of study at all. It gives a brief sketch of the recent history and the current state of Pauline studies as of the early twenty-first century, and furthermore outlines the editor’s reasons for hope for the future of the field. Finally, it summarizes the contents of the volume according to their several main sections.
Identification and Evaluation of Wheat–Aegilops bicornis Lines with Resistance to Powdery Mildew and Stripe Rust
Authors: Wang Xiaolu , Han Ran , Chen Zhiwei , Li Jianbo , Zhu Tong , Guo Jun , Xu Wenjing , Zi Yan , Li Faji , Zhai Shengnan , Li Haosheng , Liu Jianjun , Liu Aifeng , Cheng Dungong , Song Jianmin , Jia Juqing , Ma Pengtao , Liu Cheng
Published: October 2021

Wheat pathogens, especially those causing powdery mildew and stripe rust, seriously threaten yield worldwide. Utilizing newly identified disease resistance genes from wheat relatives is an effective strategy to minimize disease damage. In this study, chromosome-specific molecular markers for the 3Sb and 7Sb chromosomes of Aegilops bicornis were developed using PCR-based landmark unique gene primers for screening wheat–A. bicornis progenies. Fluorescence in situ hybridization (FISH) was performed to further identify wheat–A. bicornis progenies using oligonucleotides probes Oligo-pSc119.2-1, Oligo-pTa535-1, and Oligo-(GAA)8. After establishing A. bicornis 3Sb and 7Sb chromosome-specific FISH markers, Holdfast (common wheat)–A. bicornis 3Sb addition, 7Sb addition, 3Sb(3A) substitution, 3Sb(3B) substitution, 3Sb(3D) substitution, 7Sb(7A) substitution, and 7Sb(7B) substitution lines were identified by the molecular and cytological markers. Stripe rust and powdery mildew resistance, along with agronomic traits, were investigated to evaluate the breeding potential of these lines. Holdfast and Holdfast–A. bicornis progenies were all highly resistant to stripe rust, indicating that the stripe rust resistance might derive from Holdfast. However, Holdfast–A. bicornis 3Sb addition, 3Sb(3A) substitution, 3Sb(3B) substitution, and 3Sb(3D) substitution lines showed high resistance to powdery mildew while Holdfast was highly susceptible, indicating that chromosome 3Sb of A. bicornis carries previously unknown powdery mildew resistance gene(s). Additionally, the transfer of the 3Sb chromosome from A. bicornis to wheat significantly increased tiller number, but chromosome 7Sb has a negative effect on agronomic traits. Therefore, wheat germplasm containing A. bicornis chromosome 3Sb has potential to contribute to improving powdery mildew resistance and tiller number during wheat breeding.
Evaluation of Soybean Entries in the Pan-African Trials for Response to Coniothyrium glycines, the Cause of Red Leaf Blotch
Authors: Murithi Harun M. , Pawlowski Michelle , Degu Tizazu , Hunde Deresse , Malede Molla , Obua Tonny , Mushoriwa Hapson , Coyne Danny , Tukamuhabwa Phinehas , Hartman Glen L.
Published: October 2021

Red leaf blotch (RLB), caused by the fungus Coniothyrium glycines, is an important disease of soybean known to cause yield losses across soybean-growing regions in Africa. Fungicides are one option to manage this disease, but utilization of host resistance may be a better option suited for smallholder soybean farmers in Africa. Fifty-nine soybean entries were evaluated for RLB severity in nine field locations in Ethiopia, Kenya, Uganda, and Zambia. Disease incidence was 100% and disease severity differed (P < 0.01) among entries at eight of the nine locations. Mean severity ratings ranged from 1.4 to 3.2 based on a 0-to-5 scale, with higher disease severities recorded in Ethiopia followed by Zambia. Eight of the 59 entries were common to all nine locations and had severity ratings ranging from 1.6 to 2.9. The cultivar SC Signal had the lowest RLB severity ratings in the combined analysis over locations. Based on correlations of weather variables to RLB severity, mean rainfall from planting to 30 days before assessment date had a positive correlation (r = 0.70; P = 0.035), as did mean morning maximum wind speed (r = 0.88; P = 0.016). Other variables, such as temperature and relative humidity, did not correlate to RLB severity. This is the most comprehensive report to date on the occurrence of RLB in the region, which for the first time demonstrates an association between rainfall and wind speed with RLB severity. It also represents the first extensive report evaluating soybean genotypes for resistance against RLB in multiple environments.
Genome Resource for Elsinoë batatas, the Causal Agent of Stem and Foliage Scab Disease of Sweet Potato
Authors: Zhang Xinxin , Zou Hongda , Yang Yiling , Fang Boping , Huang Lifei
Published: October 2021

Elsinoë batatas is a phytopathogenic fungus causing stem and foliage scab disease of sweet potato. At present, there is no reference genome available for E. batatas, limiting basic research for the pathogen. The present study applied the Nanopore single-molecule sequencing technology to sequence the E. batatas genome. This study reports the first high-quality genome sequence of E. batatas, with a total contig size of 26.49 Mb, 50.8% GC content, and an N50 of 2,546,814 bp. The sequences obtained serve as a reference for analysis of E. batatas isolates and provide a resource to better understand the biology of stem and foliage scab disease of sweet potato.
The nurse's role in the care of patients with cellulitis
Authors: Lucey Megan , Evans Michael M. , Riley Kiernan , Kowalchik Kaléi , Adams Lucy , DeSanto Logan
Published: October 2021

Get to know this bacterial skin infection that affects the deep dermis and subcutaneous tissue.
Clinicopathological characteristics and treatment outcomes of luminal B1 breast cancer in Taiwan
Authors: Chen Bo-Fang , Tsai Yi-Fang , Huang Chi-Cheng , Hsu Chih-Yi , Lien Pei-Ju , Wang Yu-Ling , Lin Yen-Shu , Feng Chin-Jung , King Kuang-Liang , Chiu Jen-Hwey , Chau Gar-Yang , Tseng Ling-Ming
Published: October 2021

Background:

Hormone receptor-positive, human epidermal growth factor receptor II (HER2)-negative luminal B1 breast cancer is associated with a higher risk of disease relapse than luminal A breast cancer. Therefore, we assessed and compared the distant metastasis pattern and clinical outcomes associated with luminal B1 and luminal A breast cancer in an Asian population.

Methods:

In this observational study, we assessed patients with estrogen receptor-positive, HER2-negative breast cancer who underwent surgery from 2009 to 2016. Patients were classified into luminal A or luminal B1 subsets via immunohistochemical analysis. Disease-free survival, post-metastasis survival, and overall survival were estimated; time to disease relapse and patterns of distant metastasis were compared. Risk of relapse and mortality were assessed using Cox proportional hazards model.

Results:

Patients with luminal B1 breast cancer (n = 677) were significantly younger and had larger tumors and a higher degree of affected axillary lymph nodes, lymphovascular invasion, and tumor necrosis than those with luminal A breast cancer (n = 630). Higher rates of local recurrence and distant metastasis were observed for luminal B1 (both p < 0.05); however, no difference was observed in the specific distant metastatic sites. We observed a significant increase in disease relapse risk in luminal B1 patients compared with that in luminal A (hazard ratio: 2.157, 95% CI: 1.340-3.473, p < 0.05). Patient age, tumor size, stage, lymphovascular invasion, and receiving chemotherapy and hormone therapy were independent risk factors for metastasis and recurrence. Only the luminal B1 subtype (hazard ratio: 5.653, 95% CI: 1.166-27.409, p < 0.05) and stage (hazard ratio: 3.400, 95% CI: 1.512-7.649, p < 0.05) were identified as independent risk factors for post metastatic mortality.

Conclusion:

Luminal B1 breast cancer has aggressive tumor biology compared with luminal A breast cancer in the follow-up period. However, there was no significant difference in the disease relapse pattern between the groups.
Prevalence of Iron Deficiency and Iron Administration in Left Ventricular Assist Device and Heart Transplantation Patients
Authors: Veenis Jesse F. , Radhoe Sumant P. , Roest Stefan , Caliskan Kadir , Constantinescu Alina A. , Manintveld Olivier C. , Brugts Jasper J.
Published: October 2021

Iron deficiency (ID) is a common comorbidity in heart failure (HF). In these patients, intravenous iron administration can improve clinical outcomes and quality of life (QoL). However, data on ID are lacking in patients who have transitioned toward left ventricular assist device (LVAD) or heart transplantation (HTx). All patients who underwent LVAD (n = 84) surgery or HTx (n = 67) at our center between 2012 and 2019, aged ≥18 years with a follow-up of ≥3 months, were included. Retrospectively, the prevalence of ID up to 1 year preoperatively, and up to February 2020 postoperatively, as well as all iron administrations were assessed during this period. Iron status was assessed in 61% and 51% of the LVAD and HTx patients preoperatively, and 81% and 84%, respectively, postoperatively. Of these patients, 53% and 71% of the LVAD and HTx patients preoperatively were diagnosed with ID preoperatively, and 71% and 77%, respectively, postoperatively. ID was more frequently diagnosed >3 months postoperatively. Sixty-three percent of the LVAD (mostly intravenous) and 63% of the HTx patients (mostly oral) received iron administration. ID is highly prevalent pre- and post-LVAD and HTx. It is plausible that substitution can have similar QoL gains as in regular HF patients.
Inpatient Care Unit in Children and Adolescents With Autism Spectrum Disorder
Authors: Ozbaran Burcu , Kose Sezen , Barankoglu Ilayda , Dogan Nurhak
Published: October 2021

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder that affects social interactions and behavior. The number of children and adolescents with ASD treated in mental health services has been growing in recent years. Knowing clinical and familial characteristics of hospitalized patients with ASD and multidisciplinary approach are crucial for children and adolescents mental health professionals. In this study, 253 Turkish children and adolescents, with and without ASD, treated in psychiatry inpatient care unit were examined. Applied approaches such as medical consultation areas, psychiatric management of mothers, and pharmacological treatment during hospitalization, were studied. In addition to familial and clinical characteristics of patients with ASD, the benefits and the hospitalization conditions were evaluated. Patients with ASD showed a higher tendency on having relatives with a psychiatric disorder than the patients without ASD. A significant difference was found in terms of age, sex, and intellectual functioning, whereas length of stay did not differ drastically. Also, suicide attempts were significantly higher in patients without ASD than in patients with ASD. This study eases the management of hospitalized ASD patients with giving important information of clinical and familial characteristics.
Creation of Digital Virtual Patient by Integrating CBCT, Intraoral Scan, 3D Facial Scan: An Approach to Methodology for Integration Accuracy
Authors: Park Jae Hyun , Lee Gye-Hyeong , Moon Da-Nal , Yun Kwi-Dug , Kim Jong-Cheol , Lee Kyungmin Clara
Published: October 2021

The purpose of this paper was to introduce a method for creating a digital virtual patient by combining cone-beam computed tomography (CBCT), intraoral scan, and facial scan with a high accuracy of integration. CBCT scan, facial scan, and intraoral scan were obtained from initial visit. The virtual patient was created using the integration of these imaging modalities. Once the virtual patient was generated, digital workflow could be applied to initial patient consultation, diagnosis, treatment planning, virtual tooth setup, virtual treatment simulation, and post-treatment evaluation. integration of digital technology allows clinicians to improve diagnosis and treatment outcome. in addition, it allows for favorable patient communication. This technique eliminates the traditional impression process and complicated laboratory procedures for evaluating patient's occlusion during smile and habitual resting position. Based on this protocol, it is possible to create a digital virtual patient using CBCT, intraoral scan, and facial scan with a high accuracy of integration. it would be helpful for precision diagnosis and accurate treatment as well as favorable communication with patient.
Heterologous SARS-CoV-2 Booster Vaccinations – Preliminary Report
Authors: Atmar Robert L. , Lyke Kirsten E. , Deming Meagan E. , Jackson Lisa A. , Branche Angela R. , El Sahly Hana M. , Rostad Christina A. , Martin Judith M. , Johnston Christine , Rupp Richard E. , Mulligan Mark J. , Brady Rebecca C. , Frenck Robert W. , Bäcker Martín , Kottkamp Angelica C. , Babu Tara M. , Rajakumar Kumaravel , Edupuganti Srilatha , Dobryzynski David , Posavad Christine M. , Archer Janet I. , Crandon Sonja , Nayak Seema U. , Szydlo Daniel , Zemanek Jillian , Islas Clara P. Dominguez , Brown Elizabeth R. , Suthar Mehul S. , McElrath M. Juliana , McDermott Adrian B. , O’Connell Sarah E. , Montefiori David C. , Eaton Amanda , Neuzil Kathleen M. , Stephens David S. , Roberts Paul C. , Beigel John H. ,   the DMID 21-0012 Study Group
Published: October 2021

Background

While Coronavirus disease 2019 (Covid-19) vaccines are highly effective, breakthrough infections are occurring. Booster vaccinations have recently received emergency use authorization (EUA) for certain populations but are restricted to homologous mRNA vaccines. We evaluated homologous and heterologous booster vaccination in persons who had received an EUA Covid-19 vaccine regimen.

Methods

In this phase 1/2 open-label clinical trial conducted at ten U.S. sites, adults who received one of three EUA Covid-19 vaccines at least 12 weeks prior to enrollment and had no reported history of SARS-CoV-2 infection received a booster injection with one of three vaccines (Moderna mRNA-1273 100-μg, Janssen Ad26.COV2.S 5×1010 virus particles, or Pfizer-BioNTech BNT162b2 30-μg; nine combinations). The primary outcomes were safety, reactogenicity, and humoral immunogenicity on study days 15 and 29.

Results

458 individuals were enrolled: 154 received mRNA-1273, 150 received Ad26.CoV2.S, and 153 received BNT162b2 booster vaccines. Reactogenicity was similar to that reported for the primary series. Injection site pain, malaise, headache, and myalgia occurred in more than half the participants. Booster vaccines increased the neutralizing activity against a D614G pseudovirus (4.2-76-fold) and binding antibody titers (4.6-56-fold) for all combinations; homologous boost increased neutralizing antibody titers 4.2-20-fold whereas heterologous boost increased titers 6.2-76-fold. Day 15 neutralizing and binding antibody titers varied by 28.7-fold and 20.9-fold, respectively, across the nine prime-boost combinations.

Conclusion

Homologous and heterologous booster vaccinations were well-tolerated and immunogenic in adults who completed a primary Covid-19 vaccine regimen at least 12 weeks earlier.

(Funded by National Institute of Allergy and Infectious Diseases; Clinical Trials.gov number, NCT04889209)
Chromosome-level assembly of the common vetch reference genome (Vicia sativa)
Authors: Xi Hangwei , Nguyen Vy , Ward Christopher , Liu Zhipeng , Searle Iain R.
Published: October 2021

Background

Vicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa.

Results

We applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes.

Conclusions

The high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.
A dual endosymbiosis drives nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum
Authors: Buysse Marie , Floriano Anna Maria , Gottlieb Yuval , Nardi Tiago , Comandatore Francesco , Olivieri Emanuela , Giannetto Alessia , Palomar Ana , Makepeace Ben , Bazzocchi Chiara , Cafiso Alessandra , Sassera Davide , Duron Olivier
Published: October 2021

Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions: Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.
New cycle, same old mistakes? Overlapping vs. discrete generations in long-term recurrent selection
Authors: Labroo Marlee R. , Rutkoski Jessica E.
Published: October 2021

Background

Recurrent selection is a foundational breeding method for quantitative trait improvement. It typically features rapid breeding cycles that can lead to high rates of genetic gain. In recurrent phenotypic selection, generations do not overlap, which means that breeding candidates are evaluated and considered for selection for only one cycle. With recurrent genomic selection, candidates can be evaluated based on genomic estimated breeding values indefinitely, therefore facilitating overlapping generations. Candidates with true high breeding values that were discarded in one cycle due to underestimation of breeding value could be identified and selected in subsequent cycles. The consequences of allowing generations to overlap in recurrent selection are unknown. We assessed whether maintaining overlapping and discrete generations led to differences in genetic gain for phenotypic, genomic truncation, and genomic optimum contribution recurrent selection by simulation of traits with various heritabilities and genetic architectures across fifty breeding cycles. We also assessed differences of overlapping and discrete generations in a conventional breeding scheme with multiple stages and cohorts.

Results

With phenotypic selection, overlapping generations led to decreased genetic gain compared to discrete generations due to increased selection error bias. Selected individuals, which were in the upper tail of the distribution of phenotypic values, tended to also have high absolute error relative to their true breeding value compared to the overall population. Without repeated phenotyping, these individuals erroneously believed to have high value were repeatedly selected across cycles, leading to decreased genetic gain. With genomic truncation selection, overlapping and discrete generations performed similarly as updating breeding values precluded repeatedly selecting individuals with inaccurately high estimates of breeding values in subsequent cycles. Overlapping generations did not outperform discrete generations in the presence of a positive genetic trend with genomic truncation selection, as past generations had lower mean genetic values than the current generation of selection candidates. With genomic optimum contribution selection, overlapping and discrete generations performed similarly, but overlapping generations slightly outperformed discrete generations in the long term if the targeted inbreeding rate was extremely low.

Conclusions

Maintaining discrete generations in recurrent phenotypic selection leads to increased genetic gain, especially at low heritabilities, by preventing selection error bias. With genomic truncation selection and genomic optimum contribution selection, genetic gain does not differ between discrete and overlapping generations assuming non-genetic effects are not present. Overlapping generations may increase genetic gain in the long term with very low targeted rates of inbreeding in genomic optimum contribution selection.
A multi-dataset evaluation of frame censoring for motion correction in task-based fMRI
Authors: Jones Michael S. , Zhu Zhenchen , Bajracharya Aahana , Luor Austin , Peelle Jonathan E.
Published: October 2021

Subject motion during fMRI can affect our ability to accurately measure signals of interest. In recent years, frame censoring—that is, statistically excluding motion-contaminated data within the general linear model using nuisance regressors—has appeared in several task-based fMRI studies as a mitigation strategy. However, there have been few systematic investigations quantifying its efficacy. In the present study, we compared the performance of frame censoring to several other common motion correction approaches for task-based fMRI using open data and reproducible workflows. We analyzed eight publicly-available datasets representing eleven distinct tasks in child, adolescent, and adult participants. Performance was quantified using maximum t-values in group analyses, and ROI-based mean activation and split-half reliability in single subjects. We compared frame censoring across several thresholds to the use of 6 and 24 canonical motion regressors, wavelet despiking, robust weighted least squares, and untrained ICA-based denoising, for a total of 240 separate analyses. Thresholds used to identify censored frames were based on both motion estimates (FD) and image intensity changes (DVARS). Relative to standard motion regressors, we found consistent improvements for modest amounts of frame censoring (e.g., 1–2% data loss), although these gains were frequently comparable to what could be achieved using other techniques. Importantly, no single approach consistently outperformed the others across all datasets and tasks. These findings suggest that the choice of a motion mitigation strategy depends on both the dataset and the outcome metric of interest.
Top-down predictions of visual features dynamically reverse their bottom-up processing in the occipito-ventral pathway to facilitate stimulus disambiguation and behavior
Authors: Yan Yuening , Zhan Jiayu , Ince Robin A.A. , Schyns Philippe G.
Published: October 2021

The prevalent conception of vision-for-categorization suggests an interplay of two dynamic flows of information within the occipito-ventral pathway. The bottom-up flow progressively reduces the high-dimensional input into a lower-dimensional representation that is compared with memory to produce categorization behavior. The top-down flow predicts category information (i.e. features) from memory that propagates down the same hierarchy to facilitate input processing and behavior. However, the neural mechanisms that support such dynamic feature propagation up and down the visual hierarchy and how they facilitate behavior remain unclear. Here, we studied them using a prediction experiment that cued participants (N = 11) to the spatial location (left vs. right) and spatial frequency (SF, Low, LSF, vs. High, HSF) contents of an upcoming Gabor patch. Using concurrent MEG recordings of each participant’s neural activity, we compared the top-down flow of representation of the predicted Gabor contents (i.e. left vs. right; LSF vs. HSF) to their bottom-up flow. We show (1) that top-down prediction improves speed of categorization in all participants, (2) the top-down flow of prediction reverses the bottom-up representation of the Gabor stimuli, going from deep right fusiform gyrus sources down to occipital cortex sources contra-lateral to the expected Gabor location and (3) that predicted Gabors are better represented when the stimulus is eventually shown, leading to faster categorizations. Our results therefore trace the dynamic top-down flow of a predicted visual content that chronologically and hierarchically reversed bottom-up processing, further facilitates visual representations in early visual cortex and subsequent categorization behavior.
The Hair Cell Analysis Toolbox: A machine learning-based whole cochlea analysis pipeline
Authors: Buswinka Christopher J. , Osgood Richard T. , Simikyan Rubina G. , Rosenberg David B. , Indzhykulian Artur A.
Published: October 2021

Our sense of hearing is mediated by sensory hair cells, precisely arranged and highly specialized cells subdivided into two subtypes: outer hair cells (OHCs) which amplify sound-induced mechanical vibration, and inner hair cells (IHCs) which convert vibrations into electrical signals for interpretation by the brain. One row of IHCs and three rows of OHCs are arranged tonotopically; cells at a particular location respond best to a specific frequency which decreases from base to apex of the cochlea. Loss of hair cells at a specific place affects hearing performance at the corresponding tonotopic frequency. To better understand the underlying cause of hearing loss in patients (or experimental animals) a plot of hair cell survival along the cochlear frequency map, known as a cochleogram, can be generated post-mortem, involving manually counting thousands of cells. Currently, there are no widely applicable tools for fast, unsupervised, unbiased, and comprehensive image analysis of auditory hair cells that work well either with imaging datasets containing an entire cochlea or smaller sampled regions. Current microscopy tools allow for imaging of auditory hair cells along the full length of the cochlea, often yielding more data than feasible to manually analyze. Here, we present a machine learning-based hair cell analysis toolbox for the comprehensive analysis of whole cochleae (or smaller regions of interest). The Hair Cell Analysis Toolbox (HCAT) is a software that automates common image analysis tasks such as counting hair cells, classifying them by subtype (IHCs vs OHCs), determining their best frequency based on their location along the cochlea, and generating cochleograms. These automated tools remove a considerable barrier in cochlear image analysis, allowing for faster, unbiased, and more comprehensive data analysis practices. Furthermore, HCAT can serve as a template for deep-learning-based detection tasks in other types of biological tissue: with some training data, HCAT’s core codebase can be trained to develop a custom deep learning detection model for any object on an image.
Aperiodic EEG activity masks the dynamics of neural oscillations during loss of consciousness from propofol
Authors: Brake Niklas , Duc Flavie , Rokos Alexander , Arseneau Francis , Shahiri Shiva , Khadra Anmar , Plourde Gilles
Published: October 2021

EEGs are known to provide biomarkers for consciousness. Although EEG correlates of loss of consciousness (LOC) are often ascribed to changes in neural synchrony, mounting evidence suggests that some changes result from asynchronous neural activity. By combining EEG recordings of humans undergoing propofol administration with biophysical modelling, we present here a principled decomposition of EEG changes during LOC into synchronous and asynchronous sources. Our results reveal that IPSP decay rate and mean spike rate shape aperiodic EEG features, and that propofol’s effects on these parameters largely explain the changes in EEG spectra following propofol infusion. We further show that traditional spectral EEG analysis likely conflates these effects with changes in rhythmic activity, thereby masking the true dynamics of neural synchrony. We conclude that the well-documented propofol-induced alpha rhythm in fact appears before LOC, and that the moment of LOC is uniquely correlated with the sudden appearance of a delta rhythm.
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy
Authors: Greaney Allison J. , Starr Tyler N. , Eguia Rachel T. , Loes Andrea N. , Khan Khadija , Karim Farina , Cele Sandile , Bowen John E. , Logue Jennifer K. , Corti Davide , Veesler David , Chu Helen Y. , Sigal Alex , Bloom Jesse D.
Published: October 2021

Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1.351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1.351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1.351-elicited antibodies are more focused on the “class 3” epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.