bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief Report: Dapivirine Ring HIV-1 Prevention Effectiveness for Women Engaged in Vaginal and Anal Intercourse: Insights From Mathematical Modeling
Authors: Peebles Kathryn , Brown Elizabeth R. , Hendrix Craig W. , Palanee-Phillips Thesla , van der Straten Ariane , Harkoo Ishana , Reddy Krishnaveni , Mirembe Brenda G. , Jeenarain Nitesha , Hillier Sharon L. , Baeten Jared M. , Barnabas Ruanne V. ,   for the MTN-020/ASPIRE study team
Published: October 2022

Background:
The dapivirine vaginal ring reduces the risk of HIV-1 acquisition in acts of vaginal intercourse (VI), and although it does not offer HIV-1 protection in acts of anal intercourse (AI), it may provide some overall risk reduction for women for whom most sex acts are vaginal. We estimated the protective effect of the ring among women with high ring adherence engaged in both VI and AI.

Methods:
We developed a microsimulation model using data from the MTN-020/ASPIRE trial. Among women who reported any AI, we estimated the proportion of all sex acts that were AI. Model scenarios varied this proportion among women engaged in both VI and AI from 5% to 30%, including the trial-observed median proportion of 6.3% of all acts being AI. In primary analyses, dapivirine ring efficacy was model-calibrated at 70% for vaginal exposures and assumed to be 0% for anal exposures.

Results:
Among highly adherent women for whom 6.3% of sex acts were AI, the ring reduced HIV-1 risk by 53% (interquartile range: 44, 60), with a decline to 26% (interquartile range: 16, 36) among women for whom 30% of acts were AI. Ring effectiveness was less than 40% among women for whom AI accounted for greater than 16% of all sex acts, although this represented less than 5% of all women in the ASPIRE trial.

Conclusions:
For most women, including those who engage in AI, because most HIV-1 risk occurs in acts of vaginal sex, the dapivirine vaginal ring can provide important HIV-1 protection.
Rest/Stress Intradermal Lymphoscintigraphy for the Functional Imaging of the Lymphatic System
Authors: Tartaglione Girolamo , Ieria Francesco Pio , Visconti Giuseppe , Bartoletti Roberto , Tarantino Giulio , Aloisi Daniele , Gentileschi Stefano , Salgarello Marzia 
Published: October 2022

Purpose
Lymphoscintigraphy is the criterion-standard method for diagnosing lymphedema, and there is no universally standardized imaging modality. In our center, we use a new approach: rest/stress intradermal lymphoscintigraphy.

Methods
We tested 231 consecutive patients with suspected lymphedema. All patients were studied after a complex physical therapy program to reduce edema. Two doses of 99mTc-nanocolloid were injected intradermally. Two static planar scans were taken at rest following tracer injection. Next, patients performed an isotonic muscular exercise for 2 minutes followed by postexercise scans. Subsequently, a prolonged exercise was performed for 30 to 40 minutes, after which delayed scans were taken. Abnormal patterns were distinguished into minor or major findings, according to severity.

Results
We identified superficial lymphatic vessels and regional lymph nodes in approximately 80% of limbs. Deep vessels were visualized in 26% of limbs. Minor findings were reported in 22.7% of limbs examined, whereas major findings were reported in 53.2% of limbs.

Conclusion
We observed major findings including lymph stagnation, extravasation, or dermal backflow in a significantly higher percentage of limbs with secondary lymphedema than in primary. We also observed the deep lymphatic pathways in a significantly higher percentage of limbs with primary lymphedema. Intradermal radiotracer injection, combined with isotonic muscular exercise, may offer a better and faster imaging of lymphatic pathways, evaluating the effects of muscular exercise on lymphatic drainage. Based on the in-depth information of the lymphatic pathways provided by rest/stress intradermal lymphoscintigraphy, microsurgeons can obtain important functional information to perform supermicrosurgical lymphatic-venous anastomosis or vascularized lymph node transfer.
Facial Defects With Infraorbital and Zygomatic Area Reconstruction Using an Expanded Flap Based on the Orbicularis Oculi Muscle: A Long-Term Follow-up
Authors: Luo Si-Si , Yang Zhe , Ma Ning , Wang Wei-Xin , Chen Sen , Wu Qi , Qu Si-Wei , Li Yang-Qun 
Published: October 2022

Objective:
Reconstruction of facial soft-tissue defects may pose a dilemma for plastic surgeons, as the flaps must be reliable to obtain a natural appearance while minimizing donor site morbidities. This clinical study describes a reconstructive method for infraorbital and zygomatic defects using a pre-expanded rotation flap based on the orbicularis oculi muscle (OOM).

Methods:
The surgeries were subdivided into 2 stages. In the first stage of the operation, a 100 to 200 mL expander was placed underneath the temporal area through a hairline incision. In the second stage, after adequate inflation of the expander, the pre-expanded rotation flap based on the OOM of the lower eyelid was raised from lateral to medial to cover the facial defects.

Results:
In this single-center study from February 2010 to February 2017, 16 patients underwent facial defect reconstruction using the pre-expanded flap based on the OOM. All of the defects were located at the infraorbital and zygomatic regions, and their sizes ranged from 3.0

4.0 to 7.0

14.0 cm. The causes of these defects included postburn scars (37.5%), melanocytic nevus (50%), and hemangiomas (12.5%). In all cases, good coverage was provided for the defects that were in the medial cheek or lower eyelids. There were no flap losses of any kind. There were no major complications, and all minor incidences were treated by minimal procedures. The patients were followed up after surgery, with the follow up ranging from 6 months to 108 months. The follow-up data included postoperative consultations, the defect size, the need for further procedures and the degree of satisfaction.

Conclusion:
The pre-expanded rotation flaps in the lateral facial area based on the OOM can ideally and safely be applied for facial defect reconstruction owing to their reliable blood supply and excellent texture match.
CSF α-Synuclein and Tau as Biomarkers for Dementia With Lewy Bodies
Authors: Zhang Qinghui , Li Jia , Quan Wei , Liu Li , Qin Yidan , Pei Xiaochen , Su Hang , Xu Jing , Chen Jiajun 
Published: October 2022

Objective:
This study investigated whether α-synuclein and tau in cerebrospinal fluid (CSF) can be used as biomarkers to diagnose dementia with Lewy bodies (DLB).

Materials and Methods:
We retrieved 3303 studies with “Dementia with Lewy bodies,” “α-synuclein,” and “tau” as keywords. We formulated screening criteria, and 2 researchers completed the screening, quality evaluation, and data extraction tasks. Finally, 35 studies related to tau, and 14 studies related to α-synuclein were included. Review Manager 5.4 and Stata16 were used for meta-analysis. Subgroup, sensitivity, and meta-regression analyses were performed to identify sources of heterogeneity and strengthen the results.

Results:
Compared with the control group, DLB patients showed significantly higher CSF levels of tau [weighted mean difference=81.36 (59.82, 102.91); Z=7.40; P<0.00001], and lower CSF levels of α-synuclein [weighted mean difference=−95.25 (−162.02, −28.48); Z=2.80; P=0.005]. Mini-Mental State Examination (MMSE) score, male ratio, and disease duration were not sources of heterogeneity on subgroup and meta-regression analyses. Sensitivity analysis revealed no significant differences.

Conclusions:
Higher levels of tau and lower levels of α-synuclein were found in the CSF of patients with DLB compared with the control group. Therefore, CSF tau and α-synuclein levels may be diagnostic biomarkers for DLB.
Can the American College of Surgeons NSQIP Surgical Risk Calculator Accurately Predict Adverse Postoperative Outcomes in Emergency Abdominal Surgery? An Italian Multicenter Analysis
Authors: Scotton Giovanni , La Greca Antonio , Lirusso Chiara , Mariani Diego , Zago Mauro , Chiarugi Massimo , Tartaglia Dario , de Manzini Nicolò , Biloslavo Alan ,   for the Emergency Surgery Collaborative
Published: October 2022

Background:
The ACS-NSQIP Surgical Risk Calculator (SRC) provides an estimation of 30-day post-operative adverse outcomes. It is useful in the identification of high risk patients needing clinical optimization and supports the informed consent process. The purpose of this study is to validate its predictive value in the Italian emergency setting.

Methods:
Six Italian institutions were included. Inclusion diagnosis were acute cholecystitis, appendicitis, gastrointestinal perforation or obstruction. Areas under the ROC curves (AUC), Brier score, Hosmer-Lemershow index (H-L), and observed to expected event ratio (O/E) were measured to assess both discrimination and calibration. Effect of the Surgeon Adjustment Score (SAS) on calibration was then tested. A patient’s personal Risk Ratio (RR) was obtained and a cut-off was chosen to predict mortality with a high NPV.

Results:
2,749 emergency procedures were considered for the analysis. The AUC was 0.932 for death (0.921-0.941, p<0.0001; Brier 0.041), 0.918 for discharge to nursing or rehab facility (0.907-0.929, p<0.0001; 0.070). Discrimination was also strong (AUC>0.8) for renal failure, cardiac complication, pneumonia, venous thromboembolism, serious complication and any complication. Brier score was informative (<0.25) for all the presented variables. The O/E ratios were 1.0 for death and 0.8 for discharge to facility. For almost all other variables, there was a general risk underestimation, but the use of the SAS permitted a better calibration of the model. An RR>3.00 predicted the onset of death with sensitivity=86%, specificity=77% and NPV=99%.

Conclusions:
The ACS-NSQIP SRC has proved to be a reliable predictor of adverse post-operative outcomes also in Italian emergency settings, with particular regard to mortality. We therefore recommend the use of the SRC in the multi-disciplinary care of patients undergoing emergency abdominal surgery.
Luminal and mucosa-associated caecal microbiota of chickens after experimental Campylobacter jejuni infection in the absence of Campylobacter-specific phages of group II and III
Authors: Hankel Julia , Kittler Sophie , Chuppava Bussarakam , Galvez Eric , Strowig Till , Becker André , von Köckritz-Blickwede Maren , Plötz Madeleine , Visscher Christian 
Published: October 2022

Campylobacteriosis is still the most commonly reported zoonosis in the European Union causing gastrointestinal disease in humans. One of the most common sources for these food-borne infections is broiler meat. Interactions between

Campylobacter

(C.) jejuni and the intestinal microbiota might influence

Campylobacter

colonization in chickens. The aim of the present study was to gain further knowledge about exclusive interactions of the host microbiota with

C. jejuni

in

Campylobacter

-specific phage-free chickens under standardized conditions and special biosafety precautions.
Therefore, 12 artificially infected (

C. jejuni

inoculum with a challenge dose of 7.64 log10 c.f.u.) and 12 control chickens of the breed Ross 308 were kept under special biosafety measures in an animal facility. At day 42 of life, microbiota studies were performed on samples of caecal digesta and mucus. No

Campylobacter

-specific phages were detected by real-time PCR analysis of caecal digesta of control or artificially infected chickens. Amplification of the 16S rRNA gene was performed within the hypervariable region V4 and subsequently sequenced with Illumina MiSeq platform. R (version 4.0.2) was used to compare the microbiota between

C. jejuni

-negative and

C. jejuni

-positive chickens. The factor chickens’ infection status contributed significantly to the differences in microbial composition of mucosal samples, explaining 10.6 % of the microbiota variation (P=0.007) and in digesta samples, explaining 9.69 % of the microbiota variation (P=0.015). The strongest difference between

C. jejuni

-non-infected and

C. jejuni

-infected birds was observed for the family

Peptococcaceae

whose presence in

C. jejuni

-infected birds could not be demonstrated. Further, several genera of the family

Ruminococcaceae

appeared to be depressed in its abundance due to

Campylobacter

infection. A negative correlation was found between

Christensenellaceae

R-7 group and

Campylobacter

in

C. jejuni

-colonised chickens, both genera potentially competing for substrate. This makes

Christensenellaceae

R-7 group highly interesting for further studies that aim to find control options for

Campylobacter

infections and assess the relevance of this finding for chicken health and

Campylobacter

colonization.
Orbitofrontal Cortex is necessary for the behavioural expression, but not learning, of Pavlovian conditioned inhibition
Authors: Panayi Marios C. , Killcross Simon 
Published: October 2022

AbstractOrbitofrontal cortex (OFC) lesions cause deficits in flexible behavioural control, most notably response inhibition and has historically been linked to theories of response inhibition. This general inhibition hypothesis of OFC function has since been rejected by evidence that inhibitory behavioural control can be expressed following OFC damage, however the functional role of the OFC in the explicit learning of conditioned inhibition remains untested. Here we test whether muscimol disruption of OFC function during the learning stage of a Pavlovian conditioned inhibition procedure disrupted the learning of conditioned inhibitory associations. Muscimol abolished Inhibitory behavioural control during the learning phase, however learning about the conditioned inhibitor was intact when tested drug free in subsequent summation and retardation tests of conditioned inhibition. Muscimol also significantly impaired acquisition to control cues whose cue-outcome relationship did not change. In a second experiment, conditioned inhibition was found not to play a significant role in cue extinction (non-reinforcement), an effect that was disrupted by intra-OFC infusion of muscimol. These results confirm that the OFC is not functionally necessary for the learning of inhibitory associations but is critical to both the enhancement and suppression of responding when environmental contingencies change.
“Altered CD8+T cell associated aging gene signature in the peripheral blood of patients with Alzheimer’s disease”
Authors: Young Juan J. , Park Hong-Jai , Kim Minhyung , Par-Young Jennefer , Bartlett Hugh H. , Kim Hye Sun , Shin Min Sun , Unlu Serhan , Bucala Richard , Van Dyck Christopher H. , Allore Heather G. , Mecca Adam P. , You Sungyong , Kang Insoo 
Published: October 2022

AbstractINTRODUCTIONEffector memory (EM) CD8+T cells have been associated with poor cognition in Alzheimer’s disease (AD). Our lab recently discovered an age-associated gene expression signature of IL-7 receptor alpha (IL-7Rα)lowEM CD8+T cells. We hypothesized that individuals with AD have altered levels of this IL-7Rαlowaging gene expression.METHODSForty genes associated with IL-7RαlowEM CD8+T cells, AD, or memory, were analyzed in peripheral blood of participants with normal cognition, mild cognitive impairment, and dementia by qPCR.RESULTSOf the eight genes that were found to be differentially expressed based on clinical diagnosis, 5 genes (62.5%) were IL-7Rαlowaging genes. Principal component analysis revealed 3 clusters of participants with dementia which had distinct expression levels of IL-7Rαlowaging genes and cognitive function.DISCUSSIONOur findings support the possible relationship of the IL-7RαlowEM CD8+T cell aging signature with cognition in individuals with dementia due to AD.
RefDeduR: A text-normalization and decision-tree aided R package enabling accurate and high-throughput reference deduplication for large datasets
Authors: Shen Jiaxian , Ling Fangqiong , Hartmann Erica M. 
Published: October 2022

AbstractAs the scientific literature grows exponentially and research becomes increasingly interdisciplinary, accurate and high-throughput reference deduplication is vital in evidence synthesis studies (e.g., systematic reviews, meta-analyses) to ensure the completeness of datasets while reducing the manual screening burden. Existing tools fail to fulfill these emerging needs, as they are often labor-intensive, insufficient in accuracy, and limited to clinical fields. Here, we present RefDeduR, a text-normalization and decision-tree aided R package that enables accurate and high-throughput reference deduplication. We modularize the pipeline into text normalization, three-step exact matching, and two-step fuzzy matching processes. We also introduce a decision-tree algorithm, consider preprints when they co-exist with a peer-reviewed version, and provide actionable recommendations. Therefore, the tool is customizable, accurate, high-throughput, and practical. RefDeduR provides an effective solution to perform reference deduplication and represents a valuable advance in expanding the open-source toolkit to support evidence synthesis research.
The unique synaptic circuitry of specialized olfactory glomeruli inDrosophila melanogaster
Authors: Gruber Lydia , Cantera Rafael , Pleijzier Markus William , Steinert Michael , Pertsch Thomas , Hansson Bill S. , Rybak Jürgen 
Published: October 2022

ABSTRACTIn theDrosophilaolfactory system most odorants are encoded in the antennal lobe in a combinatory way, activating several glomerular circuits. However, odorants of particular ecological role for the fly are encoded through activation of a single specialized olfactory pathway. Comparative analyses of densely reconstructed connectomes of one broadly tuned glomerulus (DL5) and one narrowly tuned glomerulus (DA2) gained detailed insight into the variations of synaptic circuitries of glomeruli with different computational tasks. Our approach combined laser-branding of glomeruli of interest with volume based focused ion beam-scanning electron microscopy (FIB-SEM) to enable precise targeting and analysis of the two glomeruli. We discovered differences in their neuronal innervation, synaptic composition and specific circuit diagrams of their major cell types: olfactory sensory neurons (OSNs), uniglomerular projection neurons (uPNs) and multiglomerular neurons (MGNs). By comparing our data with a previously mapped narrowly tuned glomerulus (VA1v), we identified putative generic features of narrowly tuned glomerular circuits, including higher density of neuronal fibers and synapses, lower degree of OSN lateralization, stronger axo-axonic connections between OSNs, dendro-dendritic connections between many uPNs, and lower degree of presynaptic inhibition on OSN axons. In addition, this work revealed that the dendrites of the single uPN in DL5 contain a substantial amount of autapses interconnecting distant regions of the dendritic tree. The comparative analysis of glomeruli allows to formulate synaptic motifs implemented in olfactory circuits with different computational demands.
Hippocampal firing fields anchored to a moving object predict homing direction during path-integration-based behavior
Authors: Jazi Maryam Najafian , Tymorek Adrian , Yen Ting-Yun , Kavarayil Felix Jose , Stingl Moritz , Chau Sherman Richard , Baskurt Benay , Vilela Celia García , Allen Kevin 
Published: October 2022

AbstractHoming based on path integration (H-PI) is a form of navigation in which an animal uses self-motion cues to keep track of its position and return to a starting point. Despite evidence for a role of the hippocampus in H-PI, the firing patterns of hippocampal neurons associated with homing performance are unknown. Here we developed a behavioral task for mice to characterize spatially selective cells during H-PI. The task required a mouse to find a variably placed lever on an arena before returning to its home base. H-PI was assessed in complete darkness. Recordings from CA1 pyramidal neurons in mice showed that several firing fields were anchored to the lever position. The spatial stability of lever-anchored fields was reduced during trials with lower homing accuracy, and the activity of a subset of lever-anchored firing fields predicted homing direction. These results demonstrate how neurons with object-anchored firing fields contribute to navigation.
A predictive unifying explanation for nuclear shapes based on a simple geometric principle
Authors: Dickinson Richard B. , Lele Tanmay P. 
Published: October 2022

ABSTRACTNuclei have characteristic shapes dependent on cell type, which are critical for proper cell function, and nuclei lose their distinct shapes in multiple diseases including cancer, laminopathies, and progeria. Nuclear shapes result from deformations of the sub-nuclear components—nuclear lamina and chromatin. How these structures respond to cytoskeletal forces to form the nuclear shape remains unresolved. Although the mechanisms regulating nuclear shape in human tissues are not fully understood, it is known that different nuclear shapes arise from cumulative nuclear deformations post-mitosis, ranging from the rounded morphologies that develop immediately after mitosis to the various nuclear shapes that roughly correspond to cell shape (e.g., elongated nuclei in elongated cells, flat nuclei in flat cells). Here we establish a simple geometric principle of nuclear shaping: the excess surface area of the nucleus (relative to that of a sphere of the same volume) permits a wide range highly deformed nuclear shapes under the constraints of constant surface area and constant volume, and, when the lamina is smooth (tensed), the nuclear shape can be predicted entirely from these geometric constraints alone for a given cell shape. This principle explains why flattened nuclear shapes in fully spread cells are insensitive to the magnitude of the cytoskeletal forces. We demonstrate this principle by predicting limiting nuclear shapes (i.e. with smooth lamina) in various cell geometries, including isolated on a flat surface, on patterned rectangles and lines, within a monolayer, isolated in a well, or when the nucleus is impinging against a slender obstacle. We also show that the lamina surface tension and nuclear pressure can be estimated from the predicted cell and nuclear shapes when the cell cortical tension is known, and the predictions are consistent with measured forces. These results show that excess lamina surface area is the key determinant of nuclear shapes, and that nuclear shapes can be determined purely by the geometric constraints of constant (but excess) nuclear surface area and nuclear volume, not by the magnitude of the cytoskeletal forces involved.
nf-encyclopedia: A cloud-ready pipeline for chromatogram library data-independent acquisition proteomics workflows
Authors: Allen Carolyn , Meinl Rico , Searle Brian C , Just Seth , Pino Lindsay K , Fondrie William E 
Published: October 2022

AbstractData independent acquisition (DIA) mass spectrometry methods provide systematic and comprehensive quantification of the proteome; yet, relatively few open-source tools are available to analyze DIA proteomics experiments. Fewer still are tools that can leverage gas phase fractionated (GPF) chromatogram libraries to enhance the detection and quantification of peptides in these experiments. Here, we present nf-encyclopedia, an open-source NextFlow pipeline that connects three open-source tools—MSConvert, EncyclopeDIA, and MSstats—to analyze DIA proteomics experiments with or without chromatogram libraries. We demonstrate that nf-encyclopedia is reproducible both when run on a cloud platform or a local workstation and provides robust peptide and protein quantification. Additionally, we found that MSstats enhances protein-level quantitative performance over EncyclopeDIA alone. Finally, we benchmarked the ability nf-encyclopedia to scale to large experiments in the cloud by leveraging the parallelization of compute resources. The nf-encyclopedia pipeline is available under a permissive Apache 2.0 license—run it on your desktop, cluster, or in the cloud: https://github.com/TalusBio/nf-encyclopedia.