bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a new 2‐amino acid insertion in the integrase coding region of HIV‐1 subtype G isolates
Authors: Pereira‐Vaz João , Crespo Pedro , Mocho Luísa , Martinho Patrícia , Fidalgo Teresa , Correia Lurdes , Rodrigues Fernando , Duque Vítor 
Published: July 2021

AbstractAmino acid insertions have been rarely found in the integrase (IN) coding region of Human immunodeficiency virus 1 (HIV‐1), and have been considered as natural polymorphisms. It is still unclear the potential impact of these insertion mutations on the viral replication capacity and/or susceptibility to integrase strand transfer inhibitors (INSTIs). The objective of this study was to describe a previously unreported amino acid insertion in the IN coding region of HIV‐1 isolates obtained from antiretroviral treatment‐naïve infected individuals. Nucleotide sequences of HIV‐1 isolates obtained from two infected individuals were analyzed for genotypic resistance to antiretroviral drugs. Phylogenetic inference was carried out for HIV‐1 genetic variant identification. An unreported insertion of a threonine (T) and an asparagine (N) between codon 255 and 256 (S255N_TN) was identified in the IN C‐terminal domain of HIV‐1 subtype G isolates. No resistance‐associated mutations to INSTIs were detected in the inserted sequences. Both individuals maintained undetectable HIV‐1 RNA viral load, 24 months after undergoing antiretroviral treatment with an INSTI containing regimen. The results demonstrated the possibility of transmission of this insertion mutation and suggested that the codon 255 insert by itself may not affect susceptibility to INSTIs.
SARS‐CoV‐2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate?
Authors: Pascarella Stefano , Ciccozzi Massimo , Zella Davide , Bianchi Martina , Benedetti Francesca , Benvenuto Domenico , Broccolo Francesco , Cauda Roberto , Caruso Arnaldo , Angeletti Silvia , Giovanetti Marta , Cassone Antonio 
Published: July 2021

AbstractLineage B.1.617+, also known as G/452R.V3 and now denoted by WHO with the Greek letters δ and κ, is a recently described SARS‐CoV‐2 variant under investigation first identified in October 2020 in India. As of May 2021, three sublineages labeled as B.1.617.1 (κ), B.1.617.2 (δ), and B.1.617.3 have been already identified, and their potential impact on the current pandemic is being studied. This variant has 13 amino acid changes, three in its spike protein, which are currently of particular concern: E484Q, L452R, and P681R. Here, we report a major effect of the mutations characterizing this lineage, represented by a marked alteration of the surface electrostatic potential (EP) of the receptor‐binding domain (RBD) of the spike protein. Enhanced RBD‐EP is particularly noticeable in the B.1.617.2 (δ) sublineage, which shows multiple replacements of neutral or negatively charged amino acids with positively charged amino acids. We here hypothesize that this EP change can favor the interaction between the B.1.617+ RBD and the negatively charged ACE2, thus conferring a potential increase in the virus transmission.
Integrated multidisciplinary ecological analysis from the Uluzzian settlement at the Uluzzo C Rock Shelter, south‐eastern Italy
Authors: Silvestrini Sara , Romandini Matteo , Marciani Giulia , Arrighi Simona , Carrera Lisa , Fiorini Andrea , López‐García Juan Manuel , Lugli Federico , Ranaldo Filomena , Slon Viviane , Tassoni Laura , Higgins Owen Alexander , Bortolini Eugenio , Curci Antonio , Meyer Matthias , Meyer Michael Christian , Oxilia Gregorio , Zerboni Andrea , Benazzi Stefano , Spinapolice Enza Elena 
Published: July 2021

ABSTRACTThe Middle to Upper Palaeolithic transition, between 50 000 and 40 000 years ago, is a period of important ecological and cultural changes. In this framework, the Rock Shelter of Uluzzo C (Apulia, southern Italy) represents an important site due to Late Mousterian and Uluzzian evidence preserved in its stratigraphic sequence. Here, we present the results of a multidisciplinary analysis performed on the materials collected between 2016 and 2018 from the Uluzzian stratigraphic units (SUs) 3, 15 and 17. The analysis involved lithic technology, use‐wear, zooarchaeology, ancient DNA of sediments and palaeoproteomics, completed by quartz single‐grain optically stimulated luminescence dating of the cave sediments. The lithic assemblage is characterized by a volumetric production and a debitage with no or little management of the convexities (by using the bipolar technique), with the objective to produce bladelets and flakelets. The zooarchaeological study found evidence of butchery activity and of the possible exploitation of marine resources, while drawing a picture of a patchy landscape, composed of open forests and dry open environments surrounding the shelter. Ancient mitochondrial DNA from two mammalian taxa were recovered from the sediments. Preliminary zooarchaeology by mass spectrometry results are consistent with ancient DNA and zooarchaeological taxonomic information, while further palaeoproteomics investigations are ongoing. Our new data from the re‐discovery of the Uluzzo C Rock Shelter represent an important contribution to better understand the meaning of the Uluzzian in the context of the Middle/Upper Palaeolithic transition in south‐eastern Italy.
Raman measurement of the effect of lattice defects on the two‐phonon density of states in ZnO
Authors: Nour‐Al‐Deen Ibrahim , El‐Kurdi Riham , Patra Digambara , Kazan Michel 
Published: July 2021

AbstractThe resonance of the
mode of the zinc oxide (ZnO) lattice occurs near a ridge‐like structure of the two‐phonon density of states (DOS). The renormalization of the harmonic frequency of the
mode using perturbation‐theory with first‐principles calculations of the two‐phonon DOS is usually used to describe the Raman spectrum of this mode. In this contribution, we tackle the inverse problem; that is, we derive the two‐phonon DOS in ZnO using numerical analysis of Raman measurements of the
mode. We vary the temperature to displace the resonance of the
mode along the ridge and detect a wide spectrum of the two‐phonon DOS in ZnO. We first derive the two‐phonon DOS by increasing the temperature from 300 K to 1000 K with a 20 K step. Next, we perform the same study but decrease the temperature from 1000 K to 300 K to observe how the two‐phonon DOS changes due to thermal annealing. The results show that lattice defects significantly enhance the two‐phonon DOS, which highlights the need for an effective thermal management strategy when ZnO lattice defects are harnessed for technology applications.
Proton range uncertainty reduction benefits for skull base tumors in terms of normal tissue complication probability (NTCP) and healthy tissue doses
Authors: Tattenberg Sebastian , Madden Thomas M. , Gorissen Bram L. , Bortfeld Thomas , Parodi Katia , Verburg Joost 
Published: July 2021

AbstractPurposeProton therapy allows for more conformal dose distributions and lower organ at risk and healthy tissue doses than conventional photon‐based radiotherapy, but uncertainties in the proton range currently prevent proton therapy from making full use of these advantages. Numerous developments therefore aim to reduce such range uncertainties. In this work, we quantify the benefits of reductions in range uncertainty for treatments of skull base tumors.MethodsThe study encompassed 10 skull base patients with clival tumors. For every patient, six treatment plans robust to setup errors of 2 mm and range errors from 0% to 5% were created. The determined metrics included the brainstem and optic chiasm normal tissue complication probability (NTCP) with the endpoints of necrosis and blindness, respectively, as well as the healthy tissue volume receiving at least 70% of the prescription dose.ResultsA range uncertainty reduction from the current level of 4% to a potentially achievable level of 1% reduced the probability of brainstem necrosis by up to 1.3 percentage points in the nominal scenario in which neither setup nor range errors occur and by up to 2.9 percentage points in the worst‐case scenario. Such a range uncertainty reduction also reduced the optic chiasm NTCP with the endpoint of blindness by up to 0.9 percentage points in the nominal scenario and by up to 2.2 percentage points in the worst‐case scenario. The decrease in the healthy tissue volume receiving at least 70% of the prescription dose ranged from −7.8 to 24.1 cc in the nominal scenario and from −3.4 to 38.4 cc in the worst‐case scenario.ConclusionThe benefits quantified as part of this study serve as a guideline of the OAR and healthy tissue dose benefits that range monitoring techniques may be able to achieve. Benefits were observed between all levels of range uncertainty. Even smaller range uncertainty reductions may therefore be beneficial.
Changes in mood and health‐related quality of life in Look AHEAD 6 years after termination of the lifestyle intervention
Authors:   The Look AHEAD Research Group, Wadden Thomas A. , Chao Ariana M. , Anderson Harelda , Annis Kirsten , Atkinson Karen , Bolin Paula , Brantley Phillip , Clark Jeanne M. , Coday Mace , Dutton Gareth , Foreyt John P. , W. Gregg Edward , Hazuda Helen P. , Hill James O. , Hubbard Van S. , Jakicic John M. , Jeffery Robert W. , Johnson Karen C. , Kahn Steven E. , Knowler William C. , Korytkowski Mary , Lewis Cora E. , Laferrère Blandine , Middelbeek Roeland J. , Munshi Medha N. , Nathan David M. , Neiberg Rebecca H. , Pilla Scott J. , Peters Anne , Pi‐Sunyer Xavier , Rejeski Jack W. , Redmon Bruce , Stewart Tiffany , Vaughan Elizabeth , Wagenknecht Lynne E. , Walkup Michael P. , Wing Rena R. , Wyatt Holly , Yanovski Susan Z. , Zhang Ping 
Published: July 2021

AbstractObjectiveThe Action for Health in Diabetes (Look AHEAD) study previously reported that intensive lifestyle intervention (ILI) reduced incident depressive symptoms and improved health‐related quality of life (HRQOL) over nearly 10 years of intervention compared with a control group (the diabetes support and education group [DSE]) in participants with type 2 diabetes and overweight or obesity. The present study compared incident depressive symptoms and changes in HRQOL in these groups for an additional 6 years following termination of the ILI in September 2012.MethodsA total of 1,945 ILI participants and 1,900 DSE participants completed at least one of four planned postintervention assessments at which weight, mood (via the Patient Health Questionnaire‐9), antidepressant medication use, and HRQOL (via the Medical Outcomes Scale, Short Form‐36) were measured.ResultsILI participants and DSE participants lost 3.1 (0.3) and 3.8 (0.3) kg [represented as mean (SE); p = 0.10], respectively, during the 6‐year postintervention follow‐up. No significant differences were observed between groups during this time in incident mild or greater symptoms of depression, antidepressant medication use, or in changes on the physical component summary or mental component summary scores of the Short Form‐36. In both groups, mental component summary scores were higher than physical component summary scores.ConclusionsPrior participation in the ILI, compared with the DSE group, did not appear to improve subsequent mood or HRQOL during 6 years of postintervention follow‐up.
Risk of depression after diagnostic prostate cancer workup – A nationwide, registry‐based study
Authors: Friberg Anne Sofie , Brasso Klaus , Larsen Signe Benzon , Andersen Elisabeth Wreford , Krøyer Anja , Helgstrand John Thomas , Røder Martin Andreas , Klemann Nina , Kessing Lars Vedel , Johansen Christoffer , Dalton Susanne Oksbjerg 
Published: July 2021

AbstractObjectiveTo compare the risk of depression after diagnostic workup for prostate cancer (PCa), regardless of the histopathologic outcome, with that of a cancer‐free population.MethodsA nationwide cohort of Danish men who had a prostatic biopsy sample in 1998–2011 was identified from the Danish Prostate Cancer Registry and compared to an age‐matched cohort from the background population. Men with other cancers, major psychiatric disorder, or prior use of antidepressants were excluded. The risk of depression defined as hospital contact for depression or prescription for antidepressants was determined from cumulative incidence functions and multivariate Cox regression models.ResultsOf 54,766 men who underwent diagnostic workup for PCa, benign results were found for 21,418 and PCa was diagnosed in 33,347. During up to 18 years of follow‐up, the adjusted hazard of depression was higher in men with PCa than in the background population, with the highest risk in the two years after diagnosis (hazard ratio (HR) 2.77, 95% CI 2.66–2.87). Comorbidity and lowest or highest income were significant risk factors for depression and the cumulative incidence was substantially higher in men with metastatic or high‐risk disease. In men with benign histopathology the HR for depression was 1.22 (95% CI 1.14–1.31) in the first two years but no different from the background population after that.ConclusionsDiagnostic workup for PCa is associated with an increased risk of depression, mainly among men with a diagnosis of PCa. Clinicians should be aware of depressive symptoms in prostate cancer patients.
Identifying treatment effect heterogeneity in dose‐finding trials using Bayesian hierarchical models
Authors: Thomas Marius , Bornkamp Björn , Ickstadt Katja 
Published: July 2021

AbstractAn important task in drug development is to identify patients, which respond better or worse to an experimental treatment. Identifying predictive covariates, which influence the treatment effect and can be used to define subgroups of patients, is a key aspect of this task. Analyses of treatment effect heterogeneity are however known to be challenging, since the number of possible covariates or subgroups is often large, while samples sizes in earlier phases of drug development are often small. In addition, distinguishing predictive covariates from prognostic covariates, which influence the response independent of the given treatment, can often be difficult. While many approaches for these types of problems have been proposed, most of them focus on the two‐arm clinical trial setting, where patients are given either the treatment or a control. In this article we consider parallel groups dose‐finding trials, in which patients are administered different doses of the same treatment. To investigate treatment effect heterogeneity in this setting we propose a Bayesian hierarchical dose–response model with covariate effects on dose–response parameters. We make use of shrinkage priors to prevent overfitting, which can easily occur, when the number of considered covariates is large and sample sizes are small. We compare several such priors in simulations and also investigate dependent modeling of prognostic and predictive effects to better distinguish these two types of effects. We illustrate the use of our proposed approach using a Phase II dose‐finding trial and show how it can be used to identify predictive covariates and subgroups of patients with increased treatment effects.
Ingenuity in packaging maintains the quality of fresh fruits and vegetables in mixed cargo exported by sea
Authors: Ikegaya Atsushi , Kosugi Toru , Toyoizumi Tomoyasu , Nagafuji Akihiko , Yamazaki Shigehiro , Arai Eiko 
Published: July 2021

AbstractGlobal agricultural exports are expected to increase in the future. Sea transportation facilitates the carrying of an incomparably large amount of cargo for a much lower cost than by air freight. However, sea transportation takes much longer and the produce quality is inferior to that transported by air. Accordingly, it is necessary to develop technologies to create a more suitable environment for sea transportation. For this reason, a method was devised in which all fruit and vegetables packaged for domestic distribution are wrapped from the outside of the package as additional packaging with a more versatile film, and an actual export demonstration using this method was conducted in this study. Namely, two sets of 28 different kinds of fruits and vegetables were prepared, one that was wrapped in additional packaging and the other with ordinary packaging. These sets were then exported from Japan's Shimizu Port to Singapore as mixed cargo. Following transportation, instrumental analysis and sensory evaluation were performed to compare the quality of the additionally packaged produce with that of the ordinarily packaged produce. This additional packaging greatly reduced the loss of fresh weight of Chinese cabbage, lettuce, cabbage and Japanese white radish. Moreover, the additional packaging reduced the drying of ‘Shine Muscat’ grape stems. However, some produce such as peaches deteriorated in quality due to slight changes in gas concentration. For many items, additional packaging can be a low‐cost option for maintaining quality when exporting fruits and vegetables packaged for routine domestic distribution.
Can metal halides be electron donors in σ‐hole and π‐hole tetrel bonds? Cooperativity with an alkaline‐earth bond
Authors: Liu Na , Li Qingzhong 
Published: July 2021

AbstractThe tetrel bond in the complexes of TH3F‐MX2 (T = C‐Sn, M = Be and Mg; X = F, Cl, and Br) and F2CO‐MX2 has been explored and it is also called carbon bond for T = C. The results show that the halogen atom of metal halide can engage in a σ‐hole interaction with TH3F and a π‐hole interaction with F2CO. A linear carbon‐bonded complex is formed between CH3F and MX2, while a cyclic structure is obtained in other complexes, where a tetrel bond coexists with an alkaline‐earth bond. The carbon bond between CH3F and MX2 is weak with interaction energy less than 9 kJ/mol, depending on the nature of M and X atoms. The alkaline‐earth bond is stronger than the tetrel bond in the cyclic complexes and both interactions display positive cooperativity. The F2CO‐MX2 complex is more stable than TH3F‐MX2, mainly due to the stronger alkaline‐earth bond in the former. The π‐hole carbon bond is also stronger than the σ‐hole carbon bond when a metal halide acts as an electron donor. Such tetrel‐bonded structures involving metal halides have been found in the Cambridge Structural Database.
An irrigation system for noninvasively estimating intrarenal pressure during flexible ureteroscopy
Authors: Shu Xiongpeng , Hua Peng , Xie Le 
Published: July 2021

AbstractBackgroundHigh intrarenal pressure (IRP) during flexible ureteroscopy (FURS) may lead to severe complications. Reported methods for measuring IRP are often inconvenient to use, expensive and involve instruments that occupy the narrow ureter.MethodsWe proposed an irrigation system, which can noninvasively estimate IRP based on the principle of fluid mechanics. To determine the feasibility of our system, we conducted irrigation experiments on a kidney phantom and a porcine kidney. The estimated IRPs were compared with the ground truth IRPs.ResultsWhen no surgical instrument was inserted into the flexible ureteroscope's working channel, our system can estimate IRP with high accuracy. When a surgical instrument was inserted, our system can approximately estimate the level of IRP.ConclusionsOur proposed irrigation system can noninvasively estimate IRP, presenting a new thought for clinical practice. In future studies, in vivo experiments are needed to further validate and improve the system.
Robotic‐assisted completion cholecystectomy: A safe and effective approach to a challenging surgical scenario – A single center retrospective cohort study
Authors: Tschuor Christoph , Lyman William B. , Passeri Michael , Salibi Patrick N. , Baimas‐George Maria , Iannitti David A. , Baker Erin H. , Vrochides Dionisios , Martinie John B. 
Published: July 2021

AbstractBackgroundReoperation following a previous subtotal or aborted cholecystectomy presents a challenging surgical scenario that has traditionally required an open completion cholecystectomy. The aim of this study was to describe an institutional experience with a robotic‐assisted approach to completion cholecystectomy.MethodsA database was retrospectively audited to identify all patients who underwent robotic‐assisted cholecystectomy performed by two hepatopancreatobiliary surgeons at a single centre from 2010 to 2019.ResultsTwenty six patients who underwent a robotic‐assisted completion cholecystectomy were identified. Median operative time was 142 min (48–247 min) with a blood loss of 50 cc (0–500 cc). Minor complications (Clavien–Dindo ≤ II 90 days) occurred in three patients (11.5%) with no major complication or mortality reported. Median hospital length of stay was 1 day (0–6 days) with one patient readmitted.ConclusionThis study represents to our knowledge the largest series of robotic‐assisted completion cholecystectomies to date. The robotic approach appears to be a safe and effective procedure associated with a low morbidity and high success rate.
Nonlinear learning‐based model predictive control supporting state and input dependent model uncertainty estimates
Authors: Wabersich Kim P. , Zeilinger Melanie N. 
Published: July 2021

AbstractWhile model predictive control (MPC) methods have proven their efficacy when applied to systems with safety specifications and physical limitations, their performance heavily relies on an accurate prediction model. As a consequence, a significant effort in the design of MPC controllers is dedicated to the modeling part and often requires advanced physical expertise. In order to facilitate the controller design, we present an MPC scheme supporting nonlinear learning‐based prediction models, that is, data‐driven models with probabilistic parameter uncertainties. A tube‐based MPC formulation in combination with an additional implicit state and input constraint forces the closed‐loop system to be operated in domains of sufficient model confidence, thereby ensuring asymptotic stability and constraint satisfaction at a prespecified level of probability. Furthermore, by relying on tube‐based MPC concepts, the proposed learning‐based MPC formulation offers a general framework for addressing different problem classes, such as economic MPC, while providing a general interface to probabilistic prediction models based, for example, on Bayesian regression or Gaussian processes. A design procedure is proposed for approximately linear systems and the efficiency of the method is illustrated using numerical examples.