bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing the Paradigm of School-Based Physical Therapist Service Delivery: Using Evidence to Support Intensive Intervention
Authors: Kinsey Erin , Curto Colleen , Glassman Dana , Sundberg Melissa , Rosemeyer Kathryn , Rapport Mary Jane 
Published: December 2021

Purpose:
The purpose of this article is to highlight the paradigm shift away from the typical model of direct service delivery of consistent frequency and duration in the school setting to accommodate an intensive progressive resistive exercise intervention. School-based physical therapists describe how they applied an evidence-based intensive intervention with multiple students in an urban public school district.

Summary of Key Points:
The school-based physical therapists had to modify the typical service delivery model and overcome other challenges to implement this intensive intervention approach. Substantial improvements in strength and functional activities were observed in multiple students and measured across several months.

Conclusions and Recommendations for Clinical Practice:
An intensive intervention model appears effective and feasible in the school setting. Evidence-based intervention approaches should be considered when the student could benefit.

Video Abstract:
For more insights from the authors, see Supplemental Digital Content 1, available at: http://links.lww.com/PPT/A339.
Do partner services linked to molecular clusters yield people with viremia or new HIV?
Authors: Schneider John A. , Hayford Christina , Hotton Anna , Tabidze Irina , Wertheim Joel O. , Ramani Santhoshini , Hallmark Camden , Morgan Ethan , Janulis Patrick , Khanna Aditya , Ozik Jonathan , Fujimoto Kayo , Flores Rey , D’aquila Rich , Benbow Nanette 
Published: December 2021

Objectives:
We examined whether molecular cluster membership was associated with public health identification of HIV transmission potential among named partners in Chicago.

Design:
Historical cohort study.

Methods:
We matched and analyzed HIV surveillance and partner services data from HIV diagnoses (2012–2016) prior to implementation of cluster detection and response interventions. We constructed molecular clusters using HIV-TRACE at a pairwise genetic distance threshold of 0.5% and identified clusters exhibiting recent and rapid growth according to the Centers for Disease Control and Prevention definition (three new cases diagnosed in past year). Factors associated with identification of partners with HIV transmission potential were examined using multivariable Poisson regression.

Results:
There were 5208 newly diagnosed index clients over this time period. Average age of index clients in clusters was 28; 47% were Black, 29% Latinx/Hispanic, 6% female and 89% MSM. Of the 537 named partners, 191 (35.6%) were linked to index cases in a cluster and of those 16% were either new diagnoses or viremic. There was no statistically significant difference in the probability of identifying partners with HIV transmission potential among index clients in a rapidly growing cluster versus those not in a cluster [adjusted relative risk 1.82, (0.81–4.06)].

Conclusion:
Partner services that were initiated from index clients in a molecular cluster yielded similar new HIV case finding or identification of those with viremia as did interviews with index clients not in clusters. It remains unclear whether these findings are due to temporal disconnects between diagnoses and cluster identification, unobserved cluster members, or challenges with partner services implementation.
Biomarkers to predict cardiovascular disease in people living with HIV
Authors: McGettrick Padraig , Mallon Patrick W.G. 
Published: December 2021

Purpose of review
Cardiovascular diseases (CVD) is one of the leading cause of morbidity and mortality in antiretroviral treated people living with HIV (PWH) with risk score algorithms based on traditional risk factors being shown to be consistently unreliable in estimating risk in this population. This review aims to examine recent data published in last 18–24 months exploring biomarkers that may be useful in identifying PWH at risk of developing CVD.

Recent findings
Ongoing research explores the association of inflammatory biomarkers with subclinical CVD with few studies examining their clinical utility in improving CVD risk prediction. Further mechanistic studies explore the role of monocyte/macrophages in CVD pathogenesis with some studies examining functional assays as better predictors of CVD risk.

Summary
Although persistent associations with inflammatory markers and CVD are demonstrated, few biomarkers have emerged as being clinically useful. Large population studies are needed to assess their utility in improving CVD risk prediction in PWH.
Progress and challenges in human papillomavirus and cervical cancer in southern Africa
Authors: Ramogola-Masire Doreen , Luckett Rebecca , Dreyer Greta 
Published: December 2021

Purpose of review
Although cervical cancer is preventable, it is the leading cancer among women in southern Africa. The association of high-risk human papillomavirus (HR-HPV) with almost all invasive cervical cancers has led to the development of effective primary and secondary prevention measures. This review focuses on updated and new evidence of the epidemiology of HPV and HPV-based secondary prevention in southern Africa.

Recent findings
HR-HPV prevalence in southern Africa differs between regions, and varies most by HIV prevalence and age. HR-HPV prevalence among women living with HIV (WLWH) is reported between 29 and 59.7%, and between 16.2 and 25.2% among women without HIV. HPV16 is the most common HR-HPV type present in invasive cervical cancers in the region; and vaccination may potentially prevent approximately 80% of these cancers. Concerning preliminary data suggests faster development of new cervical precancer within a short follow-up period.

Summary
We need tools that identify the small number of women with precancer from the many with transient HR-HPV infection in southern Africa. The high-volume of test-positive women leads to challenges in managing triage in a HR-HPV-based screening program. Longitudinal data from the entire region is urgently needed to guide effective implementation of HPV-based screening programs.
Uterine Uptake of 68Ga-FAPI-04 in Uterine Pathology and Physiology
Authors: Zhang Xiao , Song Wenyu , Qin Chunxia , Song Yangmeihui , Liu Fang , Hu Fan , Lan Xiaoli 
Published: December 2021

Purpose

68Ga-labeled fibroblast activation protein inhibitor (68Ga-FAPI-04) has been useful in the imaging of desmoplastic reaction in different tumors. As we have found that most female patients showed avid uterine uptake of 68Ga-FAPI-04, we sought to further investigate the pathological and physiological uptake of 68Ga-FAPI-04 characteristics in the uterus.

Patients and Methods
We reviewed the image data of female patients who had undergone 68Ga-FAPI-04 PET/MRI at our institute between May 22, 2020, and June 21, 2021. The characteristics of uterine uptake and clinical information were collected. The uterus with and without malignancy were compared. We further analyzed the relationship of age, uterus size, gynecological history, and 18F-FDG uptake (if performed) with 68Ga-FAPI-04 uptake.

Results
Seventy-seven patients were included in this study. Much higher cervical 68Ga-FAPI-04 accumulation was noticed in cervical cancer patients than in normal cases, and 37 more metastases were found in 68Ga-FAPI-04 PET than that in 18F-FDG. Uterine body malignancies displayed different uptake features. Two cases with the metastases to uterine body showed relative lower 68Ga-FAPI-04 activity compared with their normal uteri. Of 67 patients without malignancy, lower 68Ga-FAPI-04 uptake was noted in postmenopausal women than in reproductive and perimenopausal patients. The invasive operation or hysteromyoma may increase 68Ga-FAPI-04 uptake.

Conclusions

68Ga-FAPI-04 PET might be a promising method in cervical cancers. However, physiological uptake may limit its diagnostic value in uterine body malignancy. It should be noticed that the metastatic lesion in the uterus may show relative lower uptake of 68Ga-FAPI-04 compared with the rest of the uterus. Age, fibroids, and uterine volume may influence 68Ga-FAPI-04 uptake in the uterus. More patients with various uterine diseases could be involved to provide more differential diagnostic information.
Supernumerary Nostril: Formation of a Large Additional Nasal Cavity in an Adult Patient
Authors: Kong Tae Hyun , Kim Yong Ha 
Published: December 2021

Abstract
The supernumerary nostril is one of the rarest congenital nasal deformities. Most of the reported cases published were in young patients, and surgery was performed according to the surgeon's preference. The authors report a case of supernumerary nostril in an adult with a large additional nasal cavity and describe an effective surgical method. The operation was performed with the following steps: alar base and open rhinoplasty incisions were performed to widen the surgical field of view. An incision was made around the additional nostril in the nasal vestibule. The tract of the additional nostril was circumferentially excised, and the raw areas were approximated. The remnant portion was completely removed to combine the two nasal cavities into one. Weir excision, augmentation rhinoplasty, and tip-plasty were performed. The authors were able to obtain satisfactory aesthetic and functional effects by performing separate surgical methods for a supernumerary nostril with large additional nasal cavities in an adult.
Critical Negatively Charged Residues Are Important for the Activity of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides
Authors: Lai Alex L. , Freed Jack H. 
Published: December 2021

AbstractCoronaviruses are a major infectious disease threat, and include the human pathogens of zoonotic origin SARS-CoV (“SARS-1”), SARS-CoV-2 (“SARS-2”) and MERS-CoV (“MERS”). Entry of coronaviruses into host cells is mediated by the viral spike (S) protein. Previously, we identified that the domain immediately downstream of the S2’ cleavage site is the bona fide FP (amino acids 798-835) for SARS-1 using ESR spectroscopy technology. We also found that the SARS-1 FP induces membrane ordering in a Ca2+ dependent fashion. In this study, we want to know which residues are involved in this Ca2+ binding, to build a topological model and to understand the role of the Ca2+. We performed a systematic mutation study on the negatively charged residues on the SARS-1 FP. While all six negatively charged residues contributes to the membrane ordering activity of the FP to some extent, D812 is the most important residue. We provided a topological model of how the FP binds Ca2+ ions: both FP1 and FP2 bind one Ca2+ ion, and there are two binding sites in FP1 and three in FP2. We also found that the corresponding residue D830 in the SARS-2 FP plays a similar critical role. ITC experiments show that the binding energies between the FP and Ca2+ as well as between the FP and membranes also decreases for all mutants. The binding of Ca2+, the folding of FP and the ordering activity correlated very well across the mutants, suggesting that the function of the Ca2+ is to help to folding of FP in membranes to enhance its activity. Using a novel pseudotyped virus particle (PP)-liposome methodology, we monitored the membrane ordering induced by the FPs in the whole S proteins in its trimer form in real time. We found that the SARS-1 and SARS-2 PPs also induce membrane ordering as the separate FPs do, and the mutations of the negatively charged residues also greatly reduce the membrane ordering activity. However, the difference in kinetic between the PP and FP indicates a possible role of FP trimerization. This finding could lead to therapeutic solutions that either target the FP-calcium interaction or block the Ca2+ channel to combat the ongoing COVID-19 pandemic.
Pandemic-scale phylogenetics
Authors: Ye Cheng , Thornlow Bryan , Kramer Alexander , McBroome Jakob , Hinrichs Angie , Corbett-Detig Russell , Turakhia Yatish 
Published: December 2021

1.AbstractPhylogenetics has been central to the genomic surveillance, epidemiology and contact tracing efforts during the COVD-19 pandemic. But the massive scale of genomic sequencing has rendered the pre-pandemic tools inadequate for comprehensive phylogenetic analyses. Here, we discuss the phylogenetic package that we developed to address the needs imposed by this pandemic. The package incorporates several pandemic-specific optimization and parallelization techniques and comprises four programs: UShER, matOptimize, RIPPLES and matUtils. Using high-performance computing, UShER and matOptimize maintain and refine daily a massive mutation-annotated phylogenetic tree consisting of all SARS-CoV-2 sequences available in online repositories. With UShER and RIPPLES, individual labs – even with modest compute resources – incorporate newly-sequenced SARS-CoV-2 genomes on this phylogeny and discover evidence for recombination in real-time. With matUtils, they rapidly query and visualize massive SARS-CoV-2 phylogenies. These tools have empowered scientists worldwide to study the SARS-CoV-2 evolution and transmission at an unprecedented scale, resolution and speed.
Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
Authors: Dejnirattisai Wanwisa , Huo Jiandong , Zhou Daming , Zahradník Jiří , Supasa Piyada , Liu Chang , Duyvesteyn Helen M.E. , Ginn Helen M. , Mentzer Alexander J. , Tuekprakhon Aekkachai , Nutalai Rungtiwa , Wang Beibei , Dijokaite Aiste , Khan Suman , Avinoam Ori , Bahar Mohammad , Skelly Donal , Adele Sandra , Johnson Sile Ann , Amini Ali , Ritter Thomas , Mason Chris , Dold Christina , Pan Daniel , Assadi Sara , Bellass Adam , Omo-Dare Nikki , Koeckerling David , Flaxman Amy , Jenkin Daniel , Aley Parvinder K , Voysey Merryn , Costa Clemens Sue Ann , Naveca Felipe Gomes , Nascimento Valdinete , Nascimento Fernanda , Fernandes da Costa Cristiano , Resende Paola Cristina , Pauvolid-Correa Alex , Siqueira Marilda M. , Baillie Vicky , Serafin Natali , Ditse Zanele , Silva Kelly Da , Madhi Shabir , Nunes Marta C , Malik Tariq , Openshaw Peter JM , Baillie J Kenneth , Semple Malcolm G , Townsend Alain R , Huang Kuan-Ying A. , Tan Tiong Kit , Carroll Miles W. , Klenerman Paul , Barnes Eleanor , Dunachie Susanna J. , Constantinides Bede , Webster Hermione , Crook Derrick , Pollard Andrew J , Lambe Teresa ,   OPTIC consortium,   ISARIC4C consortium, Paterson Neil G. , Williams Mark A. , Hall David R. , Fry Elizabeth E. , Mongkolsapaya Juthathip , Ren Jingshan , Schreiber Gideon , Stuart David I. , Screaton Gavin R 
Published: December 2021

SummaryOn the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.
Investigation of Vaccine Breakthrough Infections by Vaccine strategy during the Delta Variant Wave in France
Authors: Bal Antonin , Destras Grégory , Simon Bruno , Giannoli Jean-Marc , Morfin Florence , Lina Bruno , Josset Laurence ,   IVAC study group
Published: December 2021

AbstractHerein, we describe the characteristics of vaccine breakthrough infections (VBI) in fully vaccinated individuals according to five vaccine strategies during the Delta wave in France. Inclusion criterion was a positive test at least 2 weeks after a full vaccine schedule: homologous vaccination with Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273); heterologous vaccination with Astrazeneca and Pfizer-BioNTech (ChadOx1/BNT162b2); single-dose vaccines Johnson & Johnson (Ad26.COV2.S) or Astrazeneca (ChadOx1). A total of 1630 VBI from patients fully vaccinated between February and July were included in this study. SARS-CoV-2 sequencing performed for 1366 samples showed that the delta variant represented 94.1% (1286/1366). Delta-VBI were mainly symptomatic (mild symptoms) with no difference according to the vaccine strategy (p=0.362). The median RT-PCR Ct values at diagnosis were significantly different between symptomatic and asymptomatic cases only for BNT162b2 group (17.7 (15.07, 20.51) vs 19.00 (16.00, 23.00), p=0.004). Up to 50% of VBI was classified as early-VBI (infected less than one month after full immunization) for BNT162b2, mRNA-1273, ChadOx1, and J Ad26.COV2.S. People aged 14-49 yo were overrepresented in early VBI compared to non-early VBI for BNT162b2 and mRNA-1273 (73.92% vs 37.87% for BNT162b2 and 77.78% vs 46.67 % for mRNA-1273, p<0.05). Our data emphasize a high prevalence of Delta-VBI occurring only one month after full immunization in young patients that might be related to relaxation of barrier gestures.
The Effect of Spatial Frequency on the Visual Category Representation in the Macaque Inferior Temporal Cortex
Authors: Farhang Esmaeil , Toosi Ramin , Karami Behnam , Koushki Roxana , Rezayat Ehsan , Shakerian Farideh , Noroozi Jalaledin , Dehaqani Mohammad-Reza A. 
Published: December 2021

ABSTRACTTo expand our knowledge about the object recognition, it is critical to understand the role of spatial frequency (SF) in an object representation that occurs in the inferior temporal (IT) cortex at the final stage of processing the visual information across the ventral visual pathway. Object categories are being recognized hierarchically in at least three levels of abstraction: superordinate (e.g., animal), mid-level (e.g., human face), and subordinate (e.g., face identity). Psychophysical studies have shown rapid access to mid-level category information and low SF (LSF) contents. Although the hierarchical representation of categories has been shown to exist inside the IT cortex, the impact of SF on the multi-level category processing is poorly understood. To gain a deeper understanding of the neural basis of the interaction between SF and category representations at multiple levels, we examined the neural responses within the IT cortex of macaque monkeys viewing several SF-filtered objects. Each stimulus could be either intact or bandpass filtered into either the LSF (coarse shape information) or high SF (HSF) (fine shape information) bands. We found that in both High- and Low-SF contents, the advantage of mid-level representation has not been violated. This evidence suggests that mid-level category boundary maps are strongly represented in the IT cortex and remain unaffected with respect to any changes in the frequency content of stimuli. Our observations indicate the necessity of the HSF content for the superordinate category representation inside the IT cortex. In addition, our findings reveal that the representation of global category information is more dependent on the HSF than the LSF content. Furthermore, the lack of subordinate representation in both LSF and HSF filtered stimuli compared to the intact stimuli provide strong evidence that all SF contents are necessary for fine category visual processing.
Improving replicability using interaction with laboratories: a multi-lab experimental assessment
Authors: Jaljuli Iman , Kafkafi Neri , Giladi Eliezer , Golani Ilan , Gozes Illana , Chesler Elissa J. , Bogue Molly A. , Benjamini Yoav 
Published: December 2021

AbstractExperimentation with mouse and rat models has become a central strategy for discovering mammalian gene function, and for preclinical testing of pharmacological treatments, yet the utility of any findings critically depends on their replicability in other laboratories. In previous publications we proposed a statistical approach for estimating the inter-laboratory replicability of novel discoveries made in a single laboratory. We demonstrated that previous phenotyping results from multi-lab databases can be used to derive a Genotype-by-Lab (GxL) adjustment factor to greatly enhance the replicability of the single-lab findings, for similarly measured phenotypes, even before making the effort of replicating these finding in additional laboratories.This demonstration, however, still raised several important questions that could only be answered by an additional large-scale prospective experiment: 1) Does GxL-adjustment work in single-lab experiments that were not intended to be standardized across laboratories, and with genotypes that were not included in the previous experiments? And 2) Can it be used to adjust the results of pharmacological experiments? We investigated these questions by attempting to replicate, across three laboratories, results from five single-lab studies in the Mouse Phenome Database (MPD), offering 212 comparisons, including 60 involving a pharmacological treatment: 18 mg/kg/day fluoxetine. In addition, we define and use a dimensionless GxL factor, by dividing the GxL variance by the standard deviation between animals within groups, as a more robust vehicle to transfer the adjustment from the multi-lab analysis to very different labs and genotypes.For genotype comparisons, GxL-adjustment reduced the rate of non-replicable discoveries from 60% to 12%, for the price of reducing the power to make replicable discoveries from 87% to 66%. In absolute numbers, the adjustment prevented 23 non-replicable discoveries for the price of missing only three replicated ones. Tools and data needed for deployment of this method across other mouse experiments are publicly available in MPD. Our results further point at some phenotypes as more prone to produce non-replicable results, while others, known to be more difficult to measure, are as likely to produce replicable results (once adjusted) such as the physiological measure, body weight.
Genetic conversion of a split-drive into a full-drive element
Authors: Terradas Gerard , Bennett Jared B. , Li Zhiqian , Marshall John M. , Bier Ethan 
Published: December 2021

AbstractGene-drive systems offer an important new avenue for spreading beneficial traits into wild populations. Their core components, Cas9 and guide RNA (gRNA), can either be linked within a single cassette (full gene drive, fGD) or provided in two separate elements (split gene drive, sGD) wherein the gRNA-bearing element drives in the presence of an independent static source of Cas9. We previously designed a system engineered to turn split into full gene drives. Here, we provide experimental proof-of-principle for such a convertible system inserted at the spo11 locus, which is recoded to restore gene function. In multigenerational cage studies, the reconstituted spo11 fGD cassette initially drives with slower kinetics than the unlinked sGD element (using the same Mendelian vasa-Cas9 source), but eventually reaches a similar level of final introgression. Different kinetic behaviors may result from transient fitness costs associated with individuals co-inheriting Cas9 and gRNA transgenes during the drive process.