bluuebunny/crossref_metadata_2025 huggingface dataset:
Ureaplasma urealyticumandMycoplasma hominisurogenital infections associate with semen inflammation and decreased sperm quality
Authors: Paira Daniela A , Olivera Carolina , Tissera Andrea D , Molina Rosa I , Olmedo José J , Rivero Virginia E , Saka Héctor A , Motrich Ruben D
Published: January 2023

Ureaplasma urealyticum and Mycoplasma hominis are among the most prevalent sexually transmitted infections proposed to induce urogenital inflammation and impair sperm quality. However, the topic remains controversial since contradictory findings have been reported. Herein, we performed a comprehensive analysis of U. urealyticum and M. hominis urogenital infections and their association with urogenital inflammation (i.e., leukocyte subsets and inflammatory cytokines in semen,) and sperm quality parameters in a cohort of men with couple’s primary infertility undergoing initial infertility evaluation or with lower urinary tract symptoms and no infertility-related complaints. Overall, U. urealyticum and M. hominis infection was detected in 17.0% and 23.6% of patients, respectively, whereas the coinfection was detected in 3.8% of patients only. Remarkably, similar infection frequencies were found in the different patient subpopulations analyzed. Moreover, infections were associated with elevated semen levels of TNF, IL-1β, and IL-6 and/or increased counts of total leukocytes and their subsets, including CD4 and CD8 T lymphocytes and neutrophils. In addition, M. hominis infection and the coinfection with U. urealyticum were associated with impairments in sperm quality variables. Our results indicate that U. urealyticum and M. hominis male urogenital infections induce urogenital inflammation and decrease sperm quality, thus impairing male fertility potential. Screening for U. urealyticum and M. hominis infections and performing a comprehensive analysis of different leukocyte subsets and inflammatory cytokines in semen may be clinically helpful in the diagnosis and follow-up of male urogenital infection.
Radiotherapy plus camrelizumab affects peripheral CD8 T-cell differentiation subsets expressing PD-1, TIGIT, and CTLA-4 in esophageal squamous cell carcinoma
Authors: Guo Zhoubo , Zhang Kunning , Wei Xiaoying , Li Yanqi , Ma Xiaoxue , Li Yang , Han Dong , Du Qingwu , Zhang Tian , Chen Xi , Wei Hui , Yan Cihui , Zhang Wencheng , Pang Qingsong , Wang Ping
Published: January 2023

Our previous phase Ib trial (NCT03222440) showed that radiotherapy plus the anti–PD-1 antibody camrelizumab is a safe and feasible first-line therapy for locally advanced esophageal squamous cell carcinoma. In this study, we divided peripheral CD8 T-cell differentiation subsets into 4 subpopulations (naive T cells, central memory T cells, effector memory T cells, and CD45RA+ effector memory T cells). We then investigated the influence of radiotherapy plus camrelizumab therapy on the proportions of the 4 subsets and their PD-1, TIGIT, and CTLA-4 expression as well as their proliferative activity and compared the effects with those of concurrent chemoradiotherapy. Nineteen and 15 patients with esophageal squamous cell carcinoma who received radiotherapy plus camrelizumab therapy and concurrent chemoradiotherapy, respectively, were enrolled in this study. We isolated peripheral blood mononuclear cells from these patients before treatment and longitudinally after the delivery of 40 Gy radiotherapy. Flow cytometry was conducted to detect peripheral CD8 T-cell subsets and PD-1, TIGIT, CTLA-4, and Ki67 expression levels in patients with esophageal squamous cell carcinoma. We found that radiotherapy plus camrelizumab therapy did not change the proportions of the 4 subsets or the expression of CTLA-4, but this therapy decreased PD-1 expression by the 4 subsets and TIGIT expression by effector memory T cells, as well as significantly enhanced the proliferative activity of CD8 T cells, whereas concurrent chemoradiotherapy produced different effects. In addition, we further identified peripheral biomarkers that potentially predict the outcome of radiotherapy plus camrelizumab therapy.
Low-aberration ExB deflector optics for scanning electron microscopy
Authors: Enyama Momoyo , Nishi Ryuji , Ito Hiroyuki , Yamasaki Jun
Published: January 2023

To suppress aberrations in the signal electron optics of a scanning electron microscope, we propose ExB deflector (deflector with superimposed electric and magnetic fields) optics that cancel the aberrations generated during large-angle deflection. This improves the resolution of the angle or position of the signal electrons on the sample surface, allowing them to be discriminately detected. The proposed optics consist of two ExB deflectors and a transfer system with two 4-f systems, or systems that have four times the focal length, placed between them. This configuration maintains the symmetry of the electron beam trajectory throughout the transfer system such that aberrations generated by the first ExB deflector are negated by the second. The effect of the proposed optics was confirmed using a ray-tracing simulation of the electron beam, and the aberration was reduced to at most one-tenth of that in the case with only one ExB deflector. Furthermore, as an example, we examined the implementation of the proposed ExB deflector optics to resolve the signal electron angle and found that the sample emission angle range of 80° can be resolved with an angular resolution of 1°. Therefore, the proposed ExB deflector optics can be applied to the signal electron optics of a scanning electron microscope to improve the resolution of the signal electrons.
Time-resolved electron holography and its application to an ionic liquid specimen
Authors: Iwasaki Yoh , Akase Zentaro , Shimada Keiko , Harada Ken , Shindo Daisuke
Published: January 2023

Time-resolved electron holography was implemented in a transmission electron microscope by means of electron beam gating with a parallel-plate electrostatic deflector. Stroboscopic observations were performed by accumulating gated electron interference images while applying a periodic modulation voltage to a specimen. Electric polarization in an ionic liquid specimen was observed under applied fields. While a static electric field in the specimen was reduced by the polarization of the material, an applied field modulated at 10 kHz was not screened. This indicates that time-resolved electron holography is capable of determining the frequency limit of dynamic response of polarization in materials.

Graphical Abstract
Gendered times: how gendered contexts shape campaign messages of female candidates
Authors: Bauer Nichole M , Santia Martina
Published: January 2023

We develop and test a theory of gendered political times, which argues that the gendered political climate during an election shapes the extent to which female candidates emphasize feminine or masculine traits in campaign messages. We measure gendered electoral contexts through rigorous analyses of public opinion data and news media content of the top issues during an election, and we complement these data with an analysis of the gendered traits candidates emphasize in campaign messages during U.S. congressional election cycles from 2000 through 2018. Our results suggest that feminine electoral contexts do not necessarily lead female candidates, or male candidates, to rely on feminine traits. We find that masculine electoral contexts lead female candidates to rely more heavily on feminine traits. Our results have important implications for understanding the forces that shape the way candidates develop strategic campaign messages, and the factors that ultimately influence women’s under-representation in politics.
Transesophageal echocardiography: a tool for intraoperative assessment of coronary blood flow
Authors: Garg Pankaj , Wadiwala Ishaq J , Raavi Lekhya , Mateen Nargis , Crestanello Juan , Pham Si M , Jacob Samuel
Published: January 2023

Transesophageal echocardiography (TEE) has become an indispensable part of cardiac surgery, but its potential for assessing coronary anatomy and blood flow remains underutilised. This case report presents a case of acute iatrogenic left main coronary artery obstruction following re-operative aortic valve replacement that was promptly diagnosed by intraoperative TEE and managed successfully by Bentall operation. We also emphasise the technique of TEE for coronary evaluation, its caveats and its clinical application during cardiac surgery.
Nutritional and tissue-specific regulation of cytochrome P450 CYP711AMAX1homologues and strigolactone biosynthesis in wheat
Authors: Sigalas Petros P , Buchner Peter , Thomas Stephen G , Jamois Frank , Arkoun Mustapha , Yvin Jean-Claude , Bennett Malcolm J , Hawkesford Malcolm J
Published: January 2023

Strigolactones (SLs) are a class of phytohormones regulating branching/tillering, and their biosynthesis has been associated with nutritional signals and plant adaptation to nutrient-limiting conditions. The enzymes in the SL biosynthetic pathway downstream of carlactone are of interest as they are responsible for structural diversity in SLs, particularly cytochrome P450 CYP711A subfamily members, such as MORE AXILLARY GROWTH1 (MAX1) in Arabidopsis. We identified 13 MAX1 homologues in wheat, clustering in four clades and five homoeologous subgroups. The utilization of RNA-sequencing data revealed a distinct expression pattern of MAX1 homologues in above- and below-ground tissues, providing insights into the distinct roles of MAX1 homologues in wheat. In addition, a transcriptional analysis showed that SL biosynthetic genes were systematically regulated by nitrogen supply. Nitrogen limitation led to larger transcriptional changes in the basal nodes than phosphorus limitation, which was consistent with the observed tillering suppression, as wheat showed higher sensitivity to nitrogen. The opposite was observed in roots, with phosphorus limitation leading to stronger induction of most SL biosynthetic genes compared with nitrogen limitation. The observed tissue-specific regulation of SL biosynthetic genes in response to nutritional signals is likely to reflect the dual role of SLs as rhizosphere signals and branching inhibitors.
Photosensory adaptation mechanisms in hypocotyl phototropism: how plants recognize the direction of a light source
Authors: Haga Ken , Sakai Tatsuya
Published: January 2023

Plants recognize the direction of a light source and exhibit phototropic responses. Physiological studies have predicted that differences in the light intensity received by the cells on the irradiated and shaded sides of a coleoptile or hypocotyl cause differences in the amounts of photoproduct. This hypothetical photoproduct appears to regulate a signaling pathway that controls cell elongation in which cells under lower light intensity elongate more than those under higher light intensity. This results in a bending growth toward a light source and has been proposed as the photoproduct-gradient model of phototropism. In this review, we summarize recent findings on the photosensory adaptation mechanisms involving a blue-light photoreceptor, phototropin1 (phot1), ROOT PHOTOTROPISM2, NONPHOTOTROPIC HYPOCOTYL3 (NPH3), and another photoreceptor family, the phytochromes. The current evidence demonstrates that, in addition to the transition of the phot1–NPH3 photoreceptor complexes to their active state, the presence of a certain population of the phot1–NPH3 complexes showing a steady state, even in a light environment, is essential for recognition of the light source direction in phototropism. This is consistent with the photoproduct-gradient model, and a dissociation state of the phot1–NPH3 complex would be considered an entity of the hypothetical photoproduct in this model.
Parsing human rights, promoting health equity: reflections on Colombia’s response to Venezuelan migration
Authors: Angeleri Stefano , Murphy Thérèse
Published: January 2023

Over the last 7 years, a multidimensional crisis in Venezuela has resulted in massive emigration. Over 7 million have fled the country, with more than 2.4 million seeking to settle in Colombia. Of these, as of 2021, more than 1 million were undocumented, but the situation has started to change with the implementation of an ambitious migrant regularisation scheme. Regularisation promises access to comprehensive healthcare, full educational opportunities and the formal labour market. Securing these social determinants of health is critical because social inequalities produce health inequalities—that is, systematic health differences that are preventable and thus unjust. Social medicine, social epidemiology and international human rights law agree on this, yet law-focused studies of health equity initiatives remain rare. Aiming to reverse this, we examine Colombia’s response to Venezuelan migration, including its recent migrant regularisation initiative, which was introduced in part to comply with the country’s obligations under international human rights law. The examination foregrounds what we are calling ‘legal literacy’, testing the hypothesis that advancing health equity involves asking more and better questions about international human rights law.
A new discrete dynamical friction estimator based on N-body simulations
Authors: Ma Linhao , Hopkins Philip F , Kelley Luke Zoltan , Faucher-Giguère Claude-André
Published: January 2023

A long-standing problem in galactic simulations is to resolve the dynamical friction (DF) force acting on massive black hole particles when their masses are comparable to or less than the background simulation particles. Many sub-grid models based on the traditional Chandrasekhar DF formula have been proposed, yet they suffer from fundamental ambiguities in the definition of some terms in Chandrasekhar’s formula when applied to real galaxies, as well as difficulty in evaluating continuous quantities from (spatially) discrete simulation data. In this work, we present a new sub-grid DF estimator based on the discrete nature of N-body simulations, which also avoids the ambiguously defined quantities in Chandrasekhar’s formula. We test our estimator in the gizmo code and find that it agrees well with high-resolution simulations where DF is fully captured, with negligible additional computational cost. We also compare it with a Chandrasekhar estimator and discuss its applications in real galactic simulations.
On the choice of the most suitable indicator for the assembly state of dark matter haloes through cosmic time
Authors: Vallés-Pérez David , Planelles Susana , Monllor-Berbegal Óscar , Quilis Vicent
Published: January 2023

The dynamical state and morphological features of galaxies and galaxy clusters, and their high-redshift precursors, are tightly connected with their assembly history, encoding crucial information about the formation and evolution of such cosmic structures. As a first step towards finding an optimal indicator of the assembly state of observed structures, we use a cosmological simulation of a moderate volume to critically examine the best definition of an indicator that is able to discriminate dark matter haloes undergoing mergers and/or strong accretion from haloes experimenting a relaxed evolution. Using a combination of centre offset, virial ratio, mean radial velocity, sparsity, and ellipticity of the dark matter halo, we study how the thresholds on these parameters, as well as their relative weights, should evolve with redshift to provide the best classification possible. This allows us to split a sample of haloes in a totally relaxed, a marginally relaxed and an unrelaxed subsamples. The resulting classification strongly correlates with the merging activity obtained from the analysis of complete merger trees extracted from whole simulation data. The results on how the different indicators depend on redshift and halo mass, and their optimal combination to better match the true assembly history of haloes, could constitute relevant hints to find a suitable set of indicators applicable to observational data.
Factors influencing kidney transplantation rates: a study from the ERA Registry
Authors: Boenink Rianne , Kramer Anneke , Vanholder Raymond C , Mahillo Beatriz , Massy Ziad A , Bušić Mirela , Ortiz Alberto , Stel Vianda S , Jager Kitty J ,   Survey Collaborators, Barbullushi M , Idrizi A , Watschinger B , Neuwirt H , Eller K , Kalachik O , Leschuk S , Petkevich O , Abramowicz D , Hellemans R , Wissing K M , Colenbie L , Trnacevic S , Rebic D , Resic H , Filipov J , Megerov P , Bušić M , Žunec R , Markić D , Soloukides A , Savva I , Toumasi E , Viklicky O , Reischig T , Krejčí K , Sørensen S S , Bistrup C , Skov K , Lilienthal K , Ots-Rosenberg M , Helanterä I , Koivusalo A , Hourmant M , Essig M , Frimat L , Tomadze G , Banas B , Boletis I , Sándor M , Pálsson R , Plant W , Conlon P , Cooney A , Biancone L , Cardillo M , Ziedina I , Jusinskis J , Vaiciuniene R , Dalinkeviciene E , Delicata L , Farrugia E , Radunović D , Prelević V , Tomović F , Hilbrands L , Bemelman F J , Schaefer B , Resisæter A V , Lien B , Skauby M , Dębska-Ślizień A , Durlik M , Wiecek A , Sampaio S , Romãozinho C , Jorge C , Rambabova-Bushljetikj I , Nikolov I G , Trajceska L , Tacu D , Elec A , Covic A , Zakharova E , Naumovic R , Lausevic M , Baltesová T , Žilinská Z , Dedinská I , Ponikvar J Buturović , Arnol M , Valentín M O , Domínguez-Gil B , Crespo M , Mazuecos A , Wallquist C , Lundgren T , Dickenmann M , Toz H , Aki T , Keven K , Ravanan R , Geddes C
Published: January 2023

Background

Large international differences exist in kidney transplantation (KT) rates. We aimed to investigate which factors may explain the total, deceased donor and living donor KT rates over the last decade.

Methods

KT experts from 39 European countries completed the Kidney Transplantation Rate Survey on measures and barriers and their potential effect on the KT rate in their country. In the analyses, countries were divided into low, middle and high KT rate countries based on the KT rate at the start of study period in 2010.

Results

Experts from low KT rate countries reported more frequently that they had taken measures regarding staff, equipment and facilities to increase the total KT rate compared with middle and high KT rate countries. For donor type–specific KT, the largest international differences in measures taken were reported for deceased donor KT, with middle and high KT rate countries taking more measures, such as the use of expanded criteria donor kidneys, the presence of transplantation coordinators and (inter)national exchange of donor kidneys. Once a measure was taken, experts’ opinion on its success was similar across the low, middle and high KT rate countries. Experts from low KT rate countries more often reported potential barriers, such as patients’ lack of knowledge and distrust in the healthcare system.

Conclusions

Particularly in low KT rate countries, the KT rate might be stimulated by optimizing staff, equipment and facilities. In addition, all countries may benefit from measures specific to deceased and living donors.
On the complexity of computing Markov perfect equilibrium in general-sum stochastic games
Authors: Deng Xiaotie , Li Ningyuan , Mguni David , Wang Jun , Yang Yaodong
Published: January 2023

Similar to the role of Markov decision processes in reinforcement learning, Markov games (also called stochastic games) lay down the foundation for the study of multi-agent reinforcement learning and sequential agent interactions. We introduce approximate Markov perfect equilibrium as a solution to the computational problem of finite-state stochastic games repeated in the infinite horizon and prove its PPAD-completeness. This solution concept preserves the Markov perfect property and opens up the possibility for the success of multi-agent reinforcement learning algorithms on static two-player games to be extended to multi-agent dynamic games, expanding the reign of the PPAD-complete class.
Cutting the Innovation Engine: How Federal Funding Shocks Affect University Patenting, Entrepreneurship, and Publications
Authors: Babina Tania , He Alex Xi , Howell Sabrina T , Perlman Elisabeth Ruth , Staudt Joseph
Published: January 2023

This article studies how federal funding affects the innovation outputs of university researchers. We link person-level research grants from 22 universities to patents, publications, and career outcomes from the U.S. Census Bureau. We focus on the effects of large, idiosyncratic, and temporary cuts to federal funding in a researcher’s preexisting narrow field of study. Using an event study design, we document that these negative federal funding shocks reduce high-tech entrepreneurship and publications but increase patenting. The lost publications tend to be higher quality and more basic, whereas the additional patents tend to be lower quality, less general, and more often privately assigned. These federal funding cuts lead to an increase in private funding, which partially compensates for the decline in federal funding. Together with evidence from industry-university contracts, the results suggest that federal funding cuts shift university research funding from federal to private sources and lead to innovation outputs that are less openly accessible and more often appropriated by corporate funders.
Use It or Lose It: Efficiency and Redistributional Effects of Wealth Taxation
Authors: Guvenen Fatih , Kambourov Gueorgui , Kuruscu Burhan , Ocampo Sergio , Chen Daphne
Published: January 2023

How does wealth taxation differ from capital income taxation? When the return on investment is equal across individuals, a well-known result is that the two tax systems are equivalent. Motivated by recent empirical evidence documenting persistent return heterogeneity, we revisit this question. With heterogeneity, the two tax systems typically have opposite implications for efficiency and inequality. Under capital income taxation, entrepreneurs who are more productive and therefore generate more income pay higher taxes. Under wealth taxation, entrepreneurs who have similar wealth levels pay similar taxes regardless of their productivity, which expands the tax base, shifts the tax burden toward unproductive entrepreneurs, and raises the savings rate of productive ones. This reallocation increases aggregate productivity and output. In the simulated model parameterized to match the U.S. data, replacing the capital income tax with a wealth tax in a revenue-neutral way delivers a significantly higher average welfare. Turning to optimal taxation, the optimal wealth tax (OWT) is positive and yields large welfare gains by raising efficiency and lowering inequality. In contrast, the optimal capital income tax (OKIT) is negative—a subsidy—and delivers lower welfare gains than OWT, owing to the welfare losses from higher inequality. Furthermore, when the transition path is considered, the gains from OKIT turn into significant welfare losses for existing cohorts, whereas OWT continues to deliver robust welfare gains. These results suggest that moderate wealth taxation may be a more appealing alternative than capital income taxation, which can be significantly more distorting under return heterogeneity than under the equal-returns assumption.
Prediction of damage trajectories in systemic sclerosis using group-based trajectory modelling
Authors: Baron Murray , Barbacki Ariane , Man Ada , de Vries-Bouwstra J K , Johnson Dylan , Stevens Wendy , Osman Mohammed , Wang Mianbo , Zhang Yuqing , Sahhar Joanne , Ngian Gene-Siew , Proudman Susanna , Nikpour Mandana ,   the Australian Scleroderma Interest Group and the Canadian Scleroderma Research Group, Baron M , Gyger G , Ligier S , Pope J , Larché M , Khalidi N , Massetto A , Sutton E , Man A , Rodriguez-Reyna T S , Thorne C , Fortin P R , Ikic A , Robinson D , Osman M , Jones N , LeClercq S , Docherty P , Smith D , Abu-Hakima M , Kaminska E , Fritzler M , Nikpour Mandana , Proudman Susanna , Stevens Wendy , Sahhar Joanne , Ferdowsi Nava , Morrisroe Kathleen , Ross Laura , Ngian Gene-Siew , Walker Jennifer , Roddy Janet , Host Lauren , Major Gabor
Published: January 2023

Objectives

Damage accrual in SSc can be tracked using the Scleroderma Clinical Trials Consortium Damage Index (DI). Our goal was to develop a prediction model for damage accrual in SSc patients with early disease.

Methods

Using patients with <2 years disease duration from Canada and Australia as a derivation cohort, and from the Netherlands as a validation cohort, we used group-based trajectory modelling (GBTM) to determine ‘good’ and ‘bad’ latent damage trajectories. We developed a prediction model from this analysis and applied it to patients from derivation and validation cohorts. We plotted the actual DI trajectories of the patients predicted to be in ‘good’ or ‘bad’ groups.

Results

We found that the actual trajectories of damage accumulation for lcSSc and dcSSc were very different, so we studied each subset separately. GBTM found two distinct trajectories in lcSSc and three in dcSSc. We collapsed the two worse trajectories in the dcSSc into one group and developed a prediction model for inclusion in either ‘good’ or ‘bad’ trajectories. The performance of models using only baseline DI and sex was excellent with ROC AUC of 0.9313 for lcSSc and 0.9027 for dcSSc. Using this model, we determined whether patients would fall into ‘good’ or ‘bad’ trajectory groups and then plotted their actual trajectories which showed clear differences between the predicted ‘good’ and ‘bad’ cases in both derivation and validation cohorts.

Conclusions

A simple model using only cutaneous subset, baseline DI and sex can predict damage accumulation in early SSc.
Forequarter Amputation: Reconstruction With Targeted Muscle Reinnervation to the Filet of Forearm Free Flap
Authors: Markewych Adrian , Hansdorfer Mark , Blank Alan , Kokosis George , Kurlander David E.
Published: January 2023

Forequarter amputation is a rarely indicated operation that has the potential for delayed wound healing, chronic pain, and dysfunction. Reconstruction in cases of skin and soft tissue loss may be particularly challenging. Here we present a 79-year-old female with recurrent, previously radiated left shoulder chondrosarcoma who underwent forequarter amputation with a ‘spare parts’ filet of forearm flap and targeted muscle reinnervation to the flap. The patient healed without complication and achieved reinnervation with minimal pain.
Nutritional Assessment in Patients after Gastric Electrical Stimulation (GES)
Authors: Kochar Tanureet , Cai Wenjing , Guardiola John J. , Mathur Prateek , Hassan Hamza , Atassi Hadi , Stocker Abigail , Hughes Michael , McElmurray Lindsay , Pinkston Christina , Abell Thomas L.
Published: January 2023

Background:

Gastric electrical stimulation (GES) is used for patients with drug-refractory gastroparesis (Gp) symptoms. Approximately two-thirds of patients with Gp symptoms are either overweight or obese. We aimed to assess symptoms and nutritional status pre-GES and post-GES placement in a large sample of drug-refractory Gp patients.

Methods:

We conducted a chart review of 282 patients with drug-refractory Gp who received temporary followed by permanent GES at an academic medical center. Gastrointestinal symptoms were collected by a traditional standardized PRO (0-4, 0 being asymptomatic and 4 being worst symptoms), baseline nutritional status by BMI plus subjective global assessment (SGA score A, B, C, for mild, moderate, and severe nutritional deficits), ability to tolerate diet, enteral tube access, and parenteral therapy were assessed at baseline and after permanent GES placement.

Results:

Comparing baseline with permanent, GES was found to significantly improve upper GI symptoms in all quartiles. Of the 282 patients with baseline body mass index (BMI) information, 112 (40%) patients were severely malnourished at baseline, of which 36 (32%) patients’ nutritional status improved after GES. Among all patients, 76 (68%) patients’ nutritional status remained unchanged. Many patients with high BMI were malnourished by SGA.

Conclusion:

We conclude that symptomatic patients of different BMIs showed improvement in their GI symptoms irrespective of baseline nutritional status. Severely malnourished patients were found to have an improvement in their nutritional status after GES therapy. We conclude that BMI, even if high, is not by itself a contraindication for GES therapy for symptomatic patients.
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.
Terrisporobacter hibernicus sp. nov., isolated from bovine faeces in Northern Ireland
Authors: Mitchell Molly , Nguyen Scott V. , Connor Mairead , Fairley Derek J. , Donoghue Orla , Marshall Helina , Koolman Leonard , McMullan Geoff , Schaffer Kirsten E. , McGrath John W. , Fanning Séamus
Published: January 2023

A new species of

Terrisporobacter

, a Gram-positive, spore-forming anaerobic group, proposed name Terrisporobacter hibernicus sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3T, cells of T. hibernicus sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35–40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C16 : 0 at 22.8 %. Strain MCA3T is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3T,

Terrisporobacter petrolearius

LAM0A37T and

Terrisporobacter mayombei

DSM 6539T are also included for the first time. The closed and complete genome of strain MCA3T from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of

T. mayombei

DSM 6539T and

T. petrolearius

LAM0A37T, as performed by Illumina MiSeq, provides reference genomes for these respective species of

Terrisporobacter

for the first time. DNA–DNA hybridization values (d4) of MCA3T to

Terrisporobacter glycolicus

ATCC 14880T,

T. petrolearius

LAM0A37T and

T. mayombei

DSM 6539T are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for T. hibernicus sp. nov. is MCA3T (=NCTC 14625T=LMG 32430T).
Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov.
Authors: Rai Anusha , Suresh Gandham , Ria Biswas , L Vighnesh , PK Sreya , Ipsita Sahu , Sasikala Chintalapati , Venkata Ramana Chintalapati
Published: January 2023

The members of the genus

Alcanivorax

are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus

Alcanivorax

suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of

Alcanivorax

species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the

Alcanivorax

species were well described at the species level. The phylotaxogenomic analysis showed that

Alcanivorax

species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
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

Motivation

Detection 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.

Results

We 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.

Availability

https://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

H2A.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

Purpose

COViK - 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.

Methods

We 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.

Results

21% 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.

Conclusion

Three vaccine doses remained highly effective in preventing severe disease and this protection was sustained; a fourth dose further increased protection.

Ethical review and trial registration

The 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 interest

S. 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

Introduction

Monitoring 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.

Methods

VASCO 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.

Results

37,170 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.

Conclusions

Our results show the benefit of booster vaccinations against infection, also in risk groups, although the additional protection wanes quite rapidly.

This 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

Objective

During 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 participants

A retrospective matched test-negative case-control analysis of existing data of HCPs at a private healthcare system in Pakistan.

Methods

HCPs 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.

Results

Inactivated 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)].

Conclusions

Inactivated 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.