bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frontline Medical Professionals' Ability to Recognize and Respond to Suspected Youth Sex Trafficking
Authors: Winks Kaitlin M.H. , Cerda Francisco , Rood Corey J. , Quas Jodi A. 
Published: January 2023

Objectives
Many youth sex trafficking victims visit health care facilities while being trafficked. Little is known regarding whether frontline medical professionals recognize risk factors or are aware of effective interviewing approaches to identify and intervene for youth victims. The aim of the present study was to assess frontline medical professionals' knowledge of youth sex trafficking, adolescent development, and forensically informed interviewing to provide guidance for professional training.

Methods
Two hundred seventy-seven frontline medical professionals [first responders and emergency department (ED)/clinical professionals] in Southern California completed an online survey about their background, training, perceptions of likely youth sex trafficking scenarios, knowledge of adolescent development, sex trafficking, and forensically informed interviewing.

Results
Nearly all professionals recognized risk and the need to collect additional information, yet few (1% first responders and 12% ED) recognized that risk as sex trafficking. Forty-six percent of first responders also indicated that responding to nonmedical needs was outside of their job responsibilities. A mixed model analysis of covariance revealed significant interactions of gender by domain (P = 0.01) and domain by training (P = 0.045). Women evidenced better knowledge (78% accuracy) about sex trafficking and interviewing (73%) than adolescent development (64%), whereas men were more accurate with sex trafficking (64%) than adolescent development (61%) and interviewing (62%). For domain by training, tests of within subjects' contrasts showed a quadratic relation (P = 0.02) was the best fit model, where training was most strongly associated with accuracy in sex trafficking knowledge.

Conclusions
Frontline medical professionals are lacking in their knowledge of youth sex trafficking, interviewing, and especially adolescent development. An area in which interventions can be targeted is with training (because it emerged in a significant interaction). Training could combat unrepresentative depictions of victims, improve understanding of common victim characteristics, and highlight how forensically informed interviewing can improve medical professionals' ability to gather crucial history about victims' experiences and needs.
Sensitivity of Magnetic Resonance Imaging of the Medial Longitudinal Fasciculus in Internuclear Ophthalmoplegia
Authors: Tien Chi-Wei , Donaldson Laura , Parra-Farinas Carmen , Micieli Jonathan A. , Margolin Edward 
Published: January 2023

Background:
Internuclear ophthalmoplegia (INO) is a result of insult to the medial longitudinal fasciculus (MLF). Clinicoradiological correlation in patients with INO has been reported to be poor; however, prior studies have used low resolution MRI imaging techniques and included patients with subclinical INO. We aimed to determine the sensitivity of modern MRI interpreted by a specialist neuroradiologist to detect clinically evident INO.

Methods:
A retrospective chart review of patients in 2 tertiary University-affiliated neuro-ophthalmology practices with the diagnosis of INO. MRI scans of all patients were reviewed and interpreted by a fellowship-trained neuroradiologist for the presence of lesion in MLF and concordance with the original imaging report.

Results:
Forty-five patients were included in the study: 33 with demyelinating disease, 11 with stroke, and 1 with intracranial mass. A visible MLF lesion was present in 25/33 demyelinating cases and 7/11 ischemic cases. Lesions in 2 cases in each group were identified only after review by a fellowship-trained neuroradiologist. In demyelinating INO, patients with a visible MLF lesion were more likely to show other brainstem (72%) and supratentorial (51%) white matter lesions.

Conclusions:
In 25% of patients with demyelinating INO and 33% of patients with ischemic INO, no visible lesion was identified on current high-quality MRI imaging. Review of imaging by a neuroradiologist increased the possibility of lesion been identified.
Visual Recovery in 2 Cases of Central Retinal Artery Occlusion Treated With Prompt Intra-ophthalmic Artery Fibrinolysis
Authors: Donaldson Laura , Nicholson Patrick , Margolin Edward 
Published: January 2023

Background:
Central retinal artery occlusion (CRAO) rapidly produces inner retinal ischemia and irreversible vision loss. Although many therapeutic interventions have been proposed, no interventions have proven effective in restoring vision in large randomized controlled trials and final visual outcome in most patients is very poor.

Methods:
Retrospective case series.

Results:
We describe 2 cases of CRAO occurring after uncomplicated cataract surgery under topical anesthesia and rapidly diagnosed. Both had very severe vision loss at presentation with dramatic improvement after intra-ophthalmic artery fibrinolysis administered 2.75 and 5.5 hours after symptom onset.

Conclusion:
Sudden monocular vision loss is an ophthalmologic emergency as CRAO must be ruled out and if diagnosed, rapid intervention should be performed. Devastating vision loss can be prevented if interventional neuroradiology is trained and available on a 24-hour basis for administration of local intra-arterial thrombolysis.
HQAlign: Aligning nanopore reads for SV detection using current-level modeling
Authors: Joshi Dhaivat , Diggavi Suhas , Chaisson Mark J.P. , Kannan Sreeram 
Published: January 2023

AbstractMotivationDetection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate alignment of these long reads play an important role in identifying novel SVs. Long read sequencers such as nanopore sequencing can address this problem by providing very long reads but with high error rates, making accurate alignment challenging. Many errors induced by nanopore sequencing have a bias because of the physics of the sequencing process and proper utilization of these error characteristics can play an important role in designing a robust aligner for SV detection problems. In this paper, we design and evaluate HQAlign, an aligner for SV detection using nanopore sequenced reads. The key ideas of HQAlign include (i) using basecalled nanopore reads along with the nanopore physics to improve alignments for SVs (ii) incorporating SV specific changes to the alignment pipeline (iii) adapting these into existing state-of-the-art long read aligner pipeline, minimap2 (v2.24), for efficient alignments.ResultsWe show that HQAlign captures about 4 − 6% complementary SVs across different datasets which are missed by minimap2 alignments while having a standalone performance at par with minimap2 for real nanopore reads data. For the common SV calls between HQAlign and minimap2, HQAlign improves the start and the end breakpoint accuracy for about 10 − 50% of SVs across different datasets. Moreover, HQAlign improves the alignment rate to 89.35% from minimap2 85.64% for nanopore reads alignment to recent telomere-to-telomere CHM13 assembly, and it improves to 86.65% from 83.48% for nanopore reads alignment to GRCh37 human genome.Availabilityhttps://github.com/joshidhaivat/HQAlign.git
H2A.Xmutants exhibit enhanced DNA demethylation inArabidopsis thaliana
Authors: Frost Jennifer M. , Lee Jaehoon , Hsieh Ping-Hung , Lin Samuel J. H. , Min Yunsook , Bauer Matthew , Runkel Anne M. , Cho Hyung-Taeg , Hsieh Tzung-Fu , Choi Yeonhee , Fischer Robert L. 
Published: January 2023

AbstractH2A.Xis an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway.H2A.Xreplacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci inArabidopsis thalianafemale gametophytes during reproduction, though it is not known how FACT targets DME sites. Here, we investigated whether H2AX is involved in DME- and FACT-mediated DNA demethylation during Arabidopsis reproduction. We show thath2a.xmutants are more sensitive to genotoxic stress, consistent with previous reports.H2A.Xfused to theGreen Fluorescent Protein (GFP)gene under theH2A.Xpromoter was highly expressed in newly developingArabidopsistissues, including in male and female gametophytes. We examined DNA methylation inh2a.xdeveloping seeds using whole genome bisulfite sequencing, and found that CG DNA methylation in the developing endosperm, but not the embryo, is decreased genome-wide inh2a.xmutants, predominately in transposons and intergenic DNA. Hypomethylated sites overlapped 62 % with canonical DME loci. These data indicate that H2A.X is not required for DME function, but is important for DNA methylation homeostasis in the unique chromatin environment ofArabidopsisendosperm.
Vaccine effectiveness against severe COVID-19 during the Omicron wave in Germany: Results from the COViK study
Authors: Stoliaroff-Pepin Anna , Peine Caroline , Herath Tim , Lachmann Johannes , Hellenbrand Wiebke , Perriat Delphine , Dörre Achim , Nitsche Andreas , Michel Janine , Grossegesse Marica , Hofmann Natalie , Rinner Thomas , Kohl Claudia , Brinkmann Annika , Meyer Tanja , Stern Daniel , Treindl Fridolin , Dorner Brigitte G. , Hein Sascha , Werel Laura , Hildt Eberhard , Gläser Sven , Schühlen Helmut , Isner Caroline , Peric Alexander , Ghouzi Ammar , Reichardt Annette , Janneck Matthias , Lock Guntram , Huster Dominik , Grünewald Thomas , Schaade Lars , Wichmann Ole , Harder Thomas 
Published: January 2023

AbstractPurposeCOViK - a prospective hospital-based multicenter case-control study in Germany - aims to assess the effectiveness of COVID-19 vaccines against severe disease. Here, we report vaccine effectiveness (VE) against COVID-19-caused hospitalization and intensive care treatment during the Omicron wave.MethodsWe analyzed data from 276 cases with COVID-19 and 494 control patients recruited in 13 hospitals from 1 December 2021 to 5 September 2022. We calculated crude and confounder-adjusted VE estimates.Results21% of cases (57/276) were not vaccinated, compared to 5% of controls (26/494; p < 0.001). Confounder-adjusted VE against COVID-19-caused hospitalization was 55.4% (95% CI: 12-78%), 81.5% (95% CI: 68-90%) and 95.6% (95%CI: 88-99%) after two, three and four vaccine doses, respectively. VE against hospitalization due to COVID-19 remained stable up to one year after three vaccine doses.ConclusionThree vaccine doses remained highly effective in preventing severe disease and this protection was sustained; a fourth dose further increased protection.Ethical review and trial registrationThe study was approved by the Ethics Committee of the Charité Universitätsmedizin, Berlin (EA1/063/21) and was registered at “Deutsches Register Klinischer Studien” (DRKS00025004).Potential conflicts of interestS. G. received payment/honoraria from Astra Zeneca, Boehringer Ingelheim, Roche Pharma, Novartis and Berlin Chemie, this had no influence on this work; all other authors reported no conflicts of interest.
Vaccine effectiveness of primary and booster COVID-19 vaccinations against SARS-CoV-2 infection in the Netherlands from 12 July 2021 to 6 June 2022: a prospective cohort study
Authors: Huiberts Anne J. , de Gier Brechje , Hoeve Christina E. , de Melker Hester E. , Hahné Susan J.M. , Hartog Gerco den , Grobbee Diederick E. , van de Wijgert Janneke H.H.M. , van den Hof Susan , Knol Mirjam J. 
Published: January 2023

AbstractIntroductionMonitoring of COVID-19 vaccine effectiveness (VE) is needed to inform vaccine policy. We estimated VE of primary vaccination, and first and second booster vaccination, against SARS-CoV-2 infection overall, and in four risk groups defined by age and medical risk condition, in the Delta and Omicron BA.1/BA.2 periods.MethodsVASCO is an ongoing prospective cohort study among vaccinated and unvaccinated Dutch adults. The primary endpoint was a self-reported positive SARS-CoV-2 test during 12 July 2021-6 June 2022. Participants with a prior SARS-CoV-2 infection, based on a positive test or serology, were excluded. We used Cox proportional hazard models with vaccination status as time-varying exposure and adjustment for age, sex, educational level, and medical risk condition. We stratified by Delta and Omicron BA.1/BA.2 periods, risk group, and time since vaccination.Results37,170 participants (mean age 57 years) were included. In the Delta period, VE <6 weeks after primary vaccination was 80% (95%CI 69-87) and decreased to 71% (65-77) after 6 months. VE increased to 96% (86-99) shortly after the first booster vaccination. In the Omicron period these estimates were 46% (22-63), 25% (8-39) and 57% (52-62), respectively. VE was 50% (34-62) <6 weeks after a second booster vaccination in participants aged ≥60 years. For the Omicron period, an interaction term between vaccination status and risk group significantly improved the model (p<0.001), with generally lower VEs for those with a medical risk condition.ConclusionsOur results show the benefit of booster vaccinations against infection, also in risk groups, although the additional protection wanes quite rapidly.SummaryThis prospective cohort study contributes to vaccine policy of COVID-19 by showing the benefit of booster vaccination in preventing SARS-CoV-2 infections, also in risk groups in which protection was generally lower, although the additional protection was rather short-lived.
Effectiveness of inactivated COVID-19 vaccines against SARS-CoV-2 infections among healthcare personnel in Pakistan: a test-negative, case-control study
Authors: Khan Unab I. , Hassan Imran , Niaz Mahnoor , Azam Syed Iqbal , Hasan Zahra , Mahmood Syed Faisal , Ali Asad 
Published: January 2023

AbstractObjectiveDuring the COVID-19 pandemic, several vaccines that were efficacious in randomized controlled trials (RCTs) were authorized for mass vaccination. In developing countries, inactivated vaccines were widely administered. While inactivated vaccines have been deemed effective in reducing disease severity, for healthcare personnel (HCPs), effectiveness against COVID-19 infections is also essential to reduce the risk to vulnerable patients and ensure a stable healthcare workforce. In addition, there are limited studies examining inactivated vaccines’ effectiveness against emerging SARS-CoV-2 variants in real-world settings. We aimed to estimate the effectiveness of inactivated vaccines (BBIBP-CorV and CoronaVac) against RT-PCR-confirmed COVID-19 infections among HCPs in the setting of emerging SARS-CoV-2 variants in Pakistan.Design, setting and participantsA retrospective matched test-negative case-control analysis of existing data of HCPs at a private healthcare system in Pakistan.MethodsHCPs tested between April 1 and September 30, 2021, were included. Each case was matched to two to six controls by the date of the RT-PCR test (± 7 days) to reduce bias. We compared demographics, reasons for testing, and vaccination status between cases and controls using chi-square for categorical variables and t-test for continuous-level data. The odds of getting a PCR-confirmed SARS-COV-2 infection were calculated using conditional logistic regression, after adjusting for age, gender, and work area. Vaccine effectiveness (VE) was calculated as percent VE using (1-OR)*100.ResultsInactivated vaccines were ineffective against COVID-19 infections ≥ 14 days after receiving the first dose [VE: 20% (95% CI: −10, 41; p=0.162)]. The vaccines showed modest effectiveness ≥ 14 days after the second dose against COVID-19 infections [VE: 33% (95% CI: 11, 50; p=0.006)], and symptomatic COVID-19 infections [VE: 36% (95% CI: 10, 54; p=0.009)].ConclusionsInactivated vaccines show modest effectiveness against COVID-19 infections in the setting of emerging VOCs. This builds a strong case for boosters and/or additional vaccination.
Preoperative Intensification Treatment in Patients with Rectal Adenocarcinoma – A Standardization of Clinical Practice
Authors: Leal-Costa Luísa , Silva Diana , Baptista Carlota , Bizarro Rita , Machete Madalena , Simões Pedro , Faria Ana , Teixeira José Alberto 
Published: January 2023

AbstractNeoadjuvant radiotherapy with concurrent fluoropyrimidines followed by surgery is considered the standard-of-care in locally advanced rectal cancer (LARC). Neoadjuvant chemo-radiotherapy (CRT) is associated with a pathological complete response (pCR) rate of 11-18%. Intensification of neoadjuvant treatment can lead to higher rates of tumor resectability and pCR, although the best therapeutic sequence is unknown.This is a prospective, single arm study which aims to standardize institutional clinical practice in accordance with international recommendations. Patients with LARC received neoadjuvant intensive treatment with concurrent CRT followed by 12 weeks of consolidation chemotherapy (ChT) with CAPOX or mFOLFOX6. Clinical response was accessed by magnetic resonance imaging (MRI) at 10 weeks, 14 weeks, and 18 weeks. If complete clinical response (cCR) was obtained, awatch-and-wait(W&W) strategy was offered; otherwise, surgery was performed. The primary endpoint was to evaluate clinical response rate after 10 weeks of intensification treatment, and its comparison with historical data. Key secondary endpoints included clinical response rate at 14 and 18 weeks, rate of patients who enter W&W strategy, rate of pCR in patients who undergo surgery, recurrence free survival (RFS), overall survival (OS), and rate of adverse effects. We present efficacy and safety preliminary results one year from the start of the study.Six patients with LARC were included. Three had a tumour in the low-rectum, two in middle-rectum and one in high-rectum. At initial magnetic resonance imaging (MRI), two had cT2, three had cT3 and one had cT4; three had cN1 and one cN2; two patients had extramural venous invasion (EMVI+) and one had mesorectal fascia involvement (MRF+).After CRT, all patients started consolidation ChT. The most common grade ≥3 AEs were neutropenia, nausea, and diarrhoea. There were no dose-limiting toxicities and all patients completed treatment. MRI at 10 weeks showed a tumour regression grade (TRG) 2 in three patients, TRG3 in two patients and TRG4 in one patient. Two patients are in the W&W surveillance protocol; one is awaiting MRI at 18 weeks; another patient awaits surgery; and of the two patients already underwent surgery, one had a ypT3N1 and the other had complete pathological response (pCR). To this date there are no recurrence or death events.These preliminary results suggests tolerability and feasibility of a neoadjuvant intensification treatment in patients with LARC.Categoriesrectal adenocarcinoma, oncology
Meta-evaluation of a whole systems programme, ActEarly: A study protocol
Authors: Mansukoski Liina , Lockyer Bridget , Creaser Amy , Sheringham Jessica , Sheard Laura , Garnett Philip , Yang Tiffany , Cookson Richard , Albert Alexandra , Islam Shahid , Shore Robert , Khan Aiysha , Twite Simon , Dawson Tania , Iqbal Halima , Skarda Ieva , Villadsen Aase , Asaria Miqdad , West Jane , Sheldon Trevor , Wright John , Bryant Maria 
Published: January 2023

AbstractIntroductionLiving in an area with high levels of child poverty predisposes children to poorer mental and physical health. ActEarly is a 5-year research programme that comprises a large number of interventions (>20) with citizen science and co-production embedded. It aims to improve the health and well-being of children and families living in two areas of the UK with high levels of deprivation; Bradford in West Yorkshire, and the London Borough of Tower Hamlets. This protocol outlines the meta-evaluation (an evaluation of evaluations) of the ActEarly programme from a systems perspective, where individual interventions are viewed as events in the wider policy system across the two geographical areas. It includes investigating the programme’s impact on early life health and well-being outcomes, interdisciplinary prevention research collaboration and capacity building, and local and national decision making.MethodsThe ActEarly meta-evaluation will follow and adapt the five iterative stages of the ‘Evaluation of Programmes in Complex Adaptive Systems’ (ENCOMPASS) framework for evaluation of public health programmes in complex adaptive systems. Theory-based and mixed-methods approaches will be used to investigate the fidelity of the ActEarly research programme, and whether, why and how ActEarly contributes to changes in the policy system, and whether alternative explanations can be ruled out. Ripple effects and systems mapping will be used to explore the relationships between interventions and their outcomes, and the degree to which the ActEarly programme encouraged interdisciplinary and prevention research collaboration as intended. A computer simulation model (“LifeSim”) will also be used to evaluate the scale of the potential long-term benefits of cross-sectoral action to tackle the financial, educational and health disadvantages faced by children in Bradford and Tower Hamlets. Together, these approaches will be used to evaluate ActEarly’s dynamic programme outputs at different system levels and measure the programme’s system changes on early life health and well-being.DiscussionThis meta-evaluation protocol presents our plans for using and adapting the ENCOMPASS-framework to evaluate the system-wide impact of the early life health and well-being programme, ActEarly. Due to the collaborative and non-linear nature of the work, we reserve the option to change and query some of our evaluation choices based on the feedback we receive from stakeholders to ensure that our evaluation remains relevant and fit for purpose.
High-dimensional phenotyping to define the genetic basis of cellular morphology
Authors: Tegtmeyer Matthew , Arora Jatin , Asgari Samira , Cimini Beth A. , Peirent Emily , Liyanage Dhara , Way Gregory , Weisbart Erin , Nathan Aparna , Amariuta Tiffany , Eggan Kevin , Haghighi Marzieh , McCarroll Steven A. , Carpenter Anne E. , Singh Shantanu , Nehme Ralda , Raychaudhuri Soumya 
Published: January 2023

AbstractThe morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combined genomic and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identified novel associations between rare protein altering variants inWASF2, TSPAN15, andPRLRwith several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirmed their role in cell morphology. Analysis of common variants yielded one significant association and nominated over 300 variants with suggestive evidence (P<10-6) of association with one or more morphology traits. Our results showed that, similar to other molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.