bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autologous Fat Grafting in Reconstructive Breast Surgery: Clinically Relevant Factors Affecting the Graft Take
Authors: Luze Hanna , Schwarz Anna , Philipp Nischwitz Sebastian , Kolb Dagmar , Bounab Kaddour , Zrim Robert , Winter Raimund , Kamolz Lars-Peter , Rappl Thomas , Kotzbeck Petra 
Published: June 2022

Abstract

Background
Autologous fat grafting is an effective tool for soft tissue augmentation in reconstructive breast surgery. Despite the major advantages of this minimally invasive approach, the unpredictability of graft survival presents challenges.

Objectives
No clear consensus on the optimal technique has yet been published and well-defined prospective studies investigating impairing factors are lacking. This aim of this study was to generate valuable fundamental data.

Methods
Ten female patients undergoing elective autologous fat grafting after nipple-sparing mastectomy were enrolled. Punch biopsies and lipoaspirates were collected from the harvest site for histologic, gene expression, and scanning electron microscopic analysis. Noninvasive Lipometer measurements determining the subcutaneous adipose tissue thickness at the graft site were used to calculate the respective take rate. Patient- and surgery-related data were acquired and correlated with the take rate.

Results
A statistically relevant correlation between the take rate and the existing mean subcutaneous adipose tissue thickness at the grafted breast prior to surgery was observed. An approximate correlation was identified regarding the number of previous grafting sessions, body weight, and BMI. No statistically significant correlation was demonstrated for age, harvest site, or the mean adipocyte size. A lower level of cell damage was observed in scanning electron microscopic samples of washed lipoaspirates; and a strong indirect correlation with the expression of the adipocyte markers FABP4 and PLIN1 was apparent.

Conclusions
Factors correlating to the take rate were identified. Future studies investigating the clinical relevance of each impairing factor are essential to contribute to the optimization of this valuable method.

Level of Evidence: 4
Generating and screeningde novocompounds against given targets using ultrafast deep learning models as core components
Authors: Zhang Haiping , Saravanan Konda Mani , Yang Yang , Wei Yanjie , Yi Pan , Zhang John Z H 
Published: June 2022

AbstractDeep learning is an artificial intelligence technique in which models express geometric transformations over multiple levels. This method has shown great promise in various fields, including drug development. The availability of public structure databases prompted the researchers to use generative artificial intelligence models to narrow down their search of the chemical space, a novel approach to chemogenomics and de novo drug development. In this study, we developed a strategy that combined an accelerated LSTM_Chem (long short-term memory for de novo compounds generation), dense fully convolutional neural network (DFCNN), and docking to generate a large number of de novo small molecular chemical compounds for given targets. To demonstrate its efficacy and applicability, six important targets that account for various human disorders were used as test examples. Moreover, using the M protease as a proof-of-concept example, we find that iteratively training with previously selected candidates can significantly increase the chance of obtaining novel compounds with higher and higher predicted binding affinities. In addition, we also check the potential benefit of obtaining reliable final de novo compounds with the help of MD simulation and metadynamics simulation. The generation of de novo compounds and the discovery of binders against various targets proposed here would be a practical and effective approach. Assessing the efficacy of these top de novo compounds with biochemical studies is promising to promote related drug development.
Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction
Authors: Vishnepolsky Boris , Grigolava Maya , Managadze Grigol , Gabrielian Andrei , Rosenthal Alex , Hurt Darrell E , Tartakovsky Michael , Pirtskhalava Malak 
Published: June 2022

Abstract
The evolution of drug-resistant pathogenic microbial species is a major global health concern. Naturally occurring, antimicrobial peptides (AMPs) are considered promising candidates to address antibiotic resistance problems. A variety of computational methods have been developed to accurately predict AMPs. The majority of such methods are not microbial strain specific (MSS): they can predict whether a given peptide is active against some microbe, but cannot accurately calculate whether such peptide would be active against a particular MS. Due to insufficient data on most MS, only a few MSS predictive models have been developed so far. To overcome this problem, we developed a novel approach that allows to improve MSS predictive models (MSSPM), based on properties, computed for AMP sequences and characteristics of genomes, computed for target MS. New models can perform predictions of AMPs for MS that do not have data on peptides tested on them. We tested various types of feature engineering as well as different machine learning (ML) algorithms to compare the predictive abilities of resulting models. Among the ML algorithms, Random Forest and AdaBoost performed best. By using genome characteristics as additional features, the performance for all models increased relative to models relying on AMP sequence-based properties only. Our novel MSS AMP predictor is freely accessible as part of DBAASP database resource at http://dbaasp.org/prediction/genome
Weather, Light and Darkness in Remote Island Policing: Expanding the Horizons of the Criminological Imagination
Authors: Souhami Anna 
Published: June 2022

Abstract
The conceptual development of criminological scholarship has been inextricable with the city. This is particularly apparent in relation to policing, where foundational ideas about police work and culture are derived almost exclusively from research in cities. But how has the ubiquity of the urban context limited our criminological imagination? Drawing on a major ethnography of policing in two remote Scottish archipelagos, this paper explores how the remote island context brings new phenomena within the scope of criminological inquiry, illuminating the selectivity of its dominant preoccupations. It explores the centrality of (1) the weather, light and darkness and (2) immersion in the physical environment in the way island officers perceive the places, people and problems they encounter, and the implications for how they exercise state power.
Case Investigation and Contact Tracing Efforts From Health Departments in the United States, November 2020 to December 2021
Authors: Stargel Alison , Taylor Melanie M , Zansky Shelley , Spencer Kimberly , Hogben Matthew , Shultz Alvin 
Published: June 2022

AbstractBackgroundSixty-four state, local, and territorial health departments (HDs) in the United States report monthly performance metrics on coronavirus disease 2019 (COVID-19) case investigation and contact tracing (CI/CT) activities. We describe national CI/CT efforts from 25 October 2020 through 24 December 2021, which included 3 peaks in COVID-19 case reporting.MethodsStandardized CI/CT data elements submitted by the 64 HDs were summarized as monthly performance metrics for each HD and the nation. These included measures of CI/CT completeness, timeliness, and workloads. We calculated contact tracing efficacy as the proportion of new cases that occurred in persons identified as contacts within the 14 days before the case was reported.ResultsA total of 44 309 796 COVID-19 cases were reported to HDs, with completed HD interviews in 18 153 353 (41%). Less than half of interviews yielded ≥1 contact. A total of 19 939 376 contacts were identified; 11 632 613 were notified (58%), with 3 618 846 undergoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing within 14 days of notification. Of the total reported cases, 2 559 383 occurred in recently identified contacts.ConclusionsWe document the resource-intense nationwide effort by US HDs to mitigate the impact of COVID-19 through CI/CT before and after vaccines became widely available. These results document the coverage and performance of CI/CT despite case surges and fluctuating workforce and workloads.
Association Between Clostridium innocuum and Antibiotic-Associated Diarrhea in Adults and Children: A Cross-sectional Study and Comparative Genomics Analysis
Authors: Cherny Kathryn E , Muscat Emily B , Balaji Aakash , Mukherjee Jayabrata , Ozer Egon A , Angarone Michael P , Hauser Alan R , Sichel Joseph S , Amponsah Emmanuel , Kociolek Larry K 
Published: June 2022

Abstract

Background
A recent study from Taiwan suggested that Clostridium innocuum may be an unrecognized cause of antibiotic-associated diarrhea (AAD) and clinically indistinguishable from Clostridioides difficile infection. Our objective was to compare C. innocuum prevalence and strain between those with AAD and asymptomatic controls.

Methods
In this cross-sectional study, we collected stool from 200 individuals with AAD and 100 asymptomatic controls. We evaluated the association between AAD and C. innocuum in stool using anaerobic culture and quantitative polymerase chain reaction (qPCR). To identify strain-specific associations with AAD, we performed whole-genome sequencing of C. innocuum isolates using Illumina MiSeq and constructed comparative genomics analyses.

Results
C. innocuum was isolated from stool of 126/300 (42%) subjects and more frequently from asymptomatic controls than AAD subjects (50/100 [50%] vs 76/200 [38%], respectively; P = .047). C. innocuum isolation frequency was not associated with AAD in either the adult or pediatric subgroups. C. innocuum and C. difficile were frequently co-prevalent in individuals with and without diarrhea. There were no phylogenetic differences or accessory genome associations between C. innocuum isolates from AAD subjects and asymptomatic controls.

Conclusions
C. innocuum was frequently isolated and at a greater frequency in asymptomatic controls than those with AAD. We did not identify strain lineages or accessory genomic elements associated with AAD. These data highlight that differentiating C. innocuum–associated diarrhea from asymptomatic colonization, and differentiating diarrhea caused by C. difficile from C. innocuum, are clinical microbiology challenges that require additional investigation to identify host-specific factors and/or biomarkers that distinguish these conditions.
Shared Decision-Making Concerning Anal Cancer Screening in Persons With Human Immunodeficiency Virus
Authors: Cachay Edward R , Gilbert Tari , Deiss Robert , Mathews Wm Christopher 
Published: June 2022

Abstract

Background
Anal high-grade squamous intraepithelial lesion (aHSIL) is the immediate precursor of anal cancer. Anal cytology is a recommended screening test to identify aHSIL among people with human immunodeficiency virus (HIV; PWH). Heterogeneity of risk for invasive anal cancer among PWH suggests the value of a shared decision-making framework regarding screening.

Methods
Using a longitudinal HIV cohort with a comprehensive anal cancer screening program, we estimated the adjusted probabilities of having aHSIL on the first anal cytology. We used logistic regression models with inverse probability weighting to account for differential screening in the cohort and to construct a predicted probability nomogram for aHSIL. Sensitivity analysis was performed to estimate aHSIL prevalence corrected for misclassification bias.

Results
Of 8139 PWH under care between 2007 and 2020, 4105 (49.8%) underwent at least 1 anal cytology test. First-time cytology aHSIL was present in 502 (12.2%) PWH. The adjusted probability of having aHSIL varied from 5% to 18% depending on patient characteristics. Prespecified factors in the aHSIL prediction model included nadir CD4 cell count, ethnicity, race, age, sex, gender identity, and HIV risk factors. The ability of the model to discriminate cytological aHSIL was modest, with an area under the curve of 0.63 (95% confidence interval, .60–.65).

Conclusions
PWH are at increased risk for aHSIL and invasive anal cancer. Risk, however, varies by patient characteristics. Individual risk factor profiles predictive of aHSIL can be modeled and operationalized as nomograms to facilitate shared decision-making conversations concerning anal cancer screening.
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission Associated With an Indoor Music Event That Required Proof of Full Vaccination Against Coronavirus Disease 2019 (COVID-19) Prior to Entry—Seattle, July 2021
Authors: Roskosky Mellisa , Moni Gwen , Kawakami Vance , Lambert Joanie , Brostrom-Smith Claire , Whitney Holly , Phu Amy , Look Jennifer , Pallickaparambil Aley , Kay Meagan , Duchin Jeff 
Published: June 2022

Abstract
In July 2021, Public Health–Seattle & King County investigated a coronavirus disease 2019 (COVID-19) outbreak at an indoor event intended for fully vaccinated individuals, revealing unvaccinated staff, limited masking, poor ventilation, and overcrowding. Supporting businesses to develop and implement comprehensive COVID-19 prevention plans is essential for reducing spread in these settings.
A Retrospective Database Analysis of Before and After Social Distancing in Relation to Pediatric Infection Rate and Healthcare Services Usage During the Coronavirus Disease 2019 Pandemic
Authors: Levy Ran , Cohen Regev , Lev-Shalem Liat , Eisenkraft Arik , Yosef Tehila Fisher 
Published: June 2022

AbstractBackgroundSocial distancing policy was introduced in Israel in 2020 to reduce the spread of coronavirus disease 2019 (COVID-19). The aim of this study was to analyze the effect of social distancing on other infections in children, by comparing disease rate and healthcare utilization before and after social distancing.MethodsThis was a before-and-after study. Within this retrospective database analysis of parallel periods in 2019 (periods 1 and 2) and 2020 (periods 3 [prelockdown period] and 4 [lockdown period]) we included all pediatric population registered in the electronic medical records of the Maccabi Healthcare Services, Israel, looking at the occurrence of non–COVID-19 infections, antibiotic purchasing, physician visits, ambulatory emergency care center visits, emergency department visits, and hospitalizations.ResultsA total of 776 828 children were included from 2019, and 777 729 from 2020. We found a lower infection rate in 2020 versus 2019. We did not find a difference in infection rate between periods 1 and 2, while there was a significant difference between periods 3 and 4. We found a significant difference between periods 2 and 4, with a higher RR than for the comparison between periods 1 and 3. There was a modest decrease in ambulatory emergency care center visits in 2020, and lower increases in emergency department visits and hospital admissions. We found decreases in antibiotic purchasing between periods 1 and 3 and between periods 2 and 4, more pronounced in 2020 than in 2019.ConclusionsAnalysis of findings before and after social distancing and masking showed reduced prevalence of non–COVID-19 pediatric infections and reduced consumption of healthcare services and antibiotics related with the lockdown period.
Forward Secure Public-key Authenticated Encryption with Conjunctive Keyword Search
Authors: Jiang Zhe , Zhang Kai , Wang Liangliang , Ning Jianting 
Published: June 2022

Abstract
Public key encryption with keyword search is a promising primitive which enables search over encrypted data in secure data outsourcing services. In traditional construction, the associated keywords may be recovered from a given trapdoor by a malicious server through keyword guessing attacks. Therefore, the notion of public-key authenticated encryption with keyword search (PAEKS) was introduced, where a sender encrypts (and authenticates) the keywords using a receiver’s public key and its secret key. In this paper, we consider the forward security for PAEKS and introduce a new primitive: forward secure public-key authenticated encryption with keyword search (FS-PAEKS), which captures the information leakage risk from previously issued queries due to the updates on the outsourced data. Technically, we embed a non-interactively agreed key into the cipher-keyword generation algorithm, and bind the cipher-keyword and the trapdoor with a set converted from algorithm-generation time. Finally, we present an efficient FS-PAEKS scheme supporting conjunctive query, and prove its forward security against chosen keyword attacks and keyword guessing attacks. To illustrate practical performance, we implement our FS-PAEKS and related PAEKS schemes based on Enron dataset in real cloud environment.
New Strategies To Improve Differential-Linear Attacks With Applications To Chaskey
Authors: Xu Yaqi , Wu Baofeng , Lin Dongdai 
Published: June 2022

Abstract
Differential-linear cryptanalysis, as the combination of differential and linear cryptanalysis, is an efficient way to attack many kinds of ciphers. Recently, various refinements to this cryptanalytic technique have been proposed, especially with good effects on ARX ciphers. In the current framework of a differential-linear attack, a cipher $E$ is often divided into three parts: a differential part $E_1$, a linear part $E_2$ and a connective part $E_m$. It is a challenging problem to deal with the connective part when building a differential-linear distinguisher, and for ARX ciphers, estimating the correlation of $ E_m $ experimentally under given input difference $\Delta _m$ and output linear mask $\Gamma _m$ is the main approach so far. In this paper, we discuss the effects of $ \Delta _{m} $ and $ \Gamma _{m} $ on the correlation of $ E_m $ for the first time. As a result, we propose a new strategy to find $\Delta _m$ and $\Gamma _m$ to build differential-linear distinguishers with high correlations for ARX ciphers based on algebraic equations derived from their round functions. For the key recovery parts of differential-linear attacks, we also find a new partitioning technique which will reduce the time complexity. Based on our new methods, we improve the differential-linear attack on 7-round Chaskey.
Short-term outcome for high-risk patients after esophagectomy
Authors: Plat Victor D , Stam Wessel T , Bootsma Boukje T , Straatman Jennifer , Klausch Thomas , Heineman David J , van der Peet Donald L , Daams Freek ,   Dutch Upper GI Cancer Audit Group
Published: June 2022

Summary
Transthoracic esophagectomy (TTE) for esophageal cancer facilitates mediastinal dissection; however, it has a significant impact on cardiopulmonary status. High-risk patients may therefore be better candidates for transhiatal esophagectomy (THE) in order to prevent serious complications. This study addressed short-term outcome following TTE and THE in patients that are considered to have a higher risk of surgery-related morbidity. This population-based study included patients who underwent a curative esophagectomy between 2011 and 2018, registered in the Dutch Upper GI Cancer Audit. The Charlson comorbidity index was used to assign patients to a low-risk (score ≤ 1) and high-risk group (score ≥ 2). Propensity score matching was applied to produce comparable groups between high-risk patients receiving TTE and THE. Primary endpoint was mortality (in-hospital/30-day mortality), secondary endpoints included morbidity and oncological outcomes. Additionally, a matched subgroup analysis was performed, including only cervical reconstructions. Of 5,438 patients, 945 and 431 high-risk patients underwent TTE and THE, respectively. After propensity score matching, mortality (6.3 vs 3.3%, P = 0.050), overall morbidity, Clavien-Dindo ≥ 3 complications, pulmonary complications, cardiac complications and re-interventions were significantly more observed after TTE compared to THE. A significantly higher mortality after TTE with a cervical reconstruction was found compared to THE (7.0 vs. 2.2%, P = 0.020). Patients with a high Charlson comorbidity index predispose for a complicated postoperative course after esophagectomy, this was more outspoken after TTE compared to THE. In daily practice, these outcomes should be balanced with the lower lymph node yield, but comparable positive node count and radicality after THE.
Histopathological validation of semi-automated myocardial scar quantification techniques for dark-blood late gadolinium enhancement magnetic resonance imaging
Authors: Nies Hedwig M J M , Gommers Suzanne , Bijvoet Geertruida P , Heckman Luuk I B , Prinzen Frits W , Vogel Gaston , Van De Heyning Caroline M , Chiribiri Amedeo , Wildberger Joachim E , Mihl Casper , Holtackers Robert J 
Published: June 2022

AbstractAimsTo evaluate the performance of various semi-automated techniques for quantification of myocardial infarct size on both conventional bright-blood and novel dark-blood late gadolinium enhancement (LGE) images using histopathology as reference standard.Methods and resultsIn 13 Yorkshire pigs, reperfused myocardial infarction was experimentally induced. At 7 weeks post-infarction, both bright-blood and dark-blood LGE imaging were performed on a 1.5 T magnetic resonance scanner. Following magnetic resonance imaging (MRI), the animals were sacrificed, and histopathology was obtained. The percentage of infarcted myocardium was assessed per slice using various semi-automated scar quantification techniques, including the signal threshold vs. reference mean (STRM, using 3 to 8 SDs as threshold) and full-width at half-maximum (FWHM) methods, as well as manual contouring, for both LGE methods. Infarct size obtained by histopathology was used as reference. In total, 24 paired LGE MRI slices and histopathology samples were available for analysis. For both bright-blood and dark-blood LGE, the STRM method with a threshold of 5 SDs led to the best agreement to histopathology without significant bias (−0.23%, 95% CI [−2.99, 2.52%], P = 0.862 and −0.20%, 95% CI [−2.12, 1.72%], P = 0.831, respectively). Manual contouring significantly underestimated infarct size on bright-blood LGE (−1.57%, 95% CI [−2.96, −0.18%], P = 0.029), while manual contouring on dark-blood LGE outperformed semi-automated quantification and demonstrated the most accurate quantification in this study (−0.03%, 95% CI [−0.22, 0.16%], P = 0.760).ConclusionThe signal threshold vs. reference mean method with a threshold of 5 SDs demonstrated the most accurate semi-automated quantification of infarcted myocardium, without significant bias compared to histopathology, for both conventional bright-blood and novel dark-blood LGE.