bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutron spectroscopy as a method for classical force-field parameterization: Past methods, present successes and future challenges
Authors: Armstrong Jeff 
Published: October 2022

Abstract
Classical molecular dynamics (MD) plays a central role in understanding structural and dynamical phenomena across all disciplines of physical chemistry. These models can be used to interpret experimental data, or as a method of study in their own right. Their legitimacy however rests solely on the accuracy of the underlying force-field, and so the parameterisation of these force-fields is the most crucial aspect of any study. The typical methods of parameterisation are structural or thermodynamic in nature, however this perspective article will examine a little used metric of parametersation; that of neutron spectroscopy, and in particular quasi-elastic neutron spectroscopy (QENS). QENS data contains self-correlation information for the hydrogen atoms of a system, over a wide range of distances and time-scales. These scales are relevant for local and global diffusion and rotation, thus pairing very well to the scales of molecular dynamics for organic systems. This article focuses in particular on the parameterisation of models of porous and surface catalysts. This area is a particularly rich field for the application of QENS, however there is a distinct lack of accurate classical force-fields currently.
Near-term potential of organic waste management infrastructure for soil carbon sequestration in rangelands
Authors: Hall A L , Potts M D , Silver W L 
Published: October 2022

Abstract
Contemporary food and agricultural systems degrade soils, pollute natural resources, and contribute to greenhouse gas emissions. The waste output from these systems, however, can be repurposed as an agricultural input, reducing emissions associated with organics disposal while actively sequestering atmospheric carbon in soils—thus transitioning the sector from a carbon source to a carbon sink. This research estimates the near-term technical and economic potential of utilizing composted organic feedstocks as a soil amendment to mitigate climate change and improve long-term soil quality, in line with California’s organics diversion policies, by connecting food scraps and organics residuals in California’s municipal solid waste to existing infrastructure and working lands in the state. The multi-objective spatial optimization results indicate considerable carbon sequestration benefits in the range of −1.9 ± 0.5 MMT CO2eq annually, by applying compost to 6 million hectares of California rangelands at a price of approximately $200 per ton, presenting a cost-effective climate change mitigation strategy within proposed federal sequestration credits. Expanding composting capacity is predicted to increase the total amount of carbon sequestered while reducing the cost per ton and per hectare treated. This model aids decision makers in considering the technical, economic, and institutional potential of actively managing the State’s organic materials in municipal waste streams for climate change mitigation.
Defect passivation and electrical conductivity enhancement in perovskite solar cells using functionalized graphene quantum dots
Authors: Rui Yichuan , Jin Zuoming , Fan Xinyi , Li Weitao , Li Bin , Li Tianpeng , Wang Yuanqiang , Wang Liang , Liang Jia 
Published: October 2022

Abstract
Organic–inorganic halide perovskites have been intensively investigated as potential photovoltaic materials due to their exceptional optoelectronic properties and their successful applications in perovskite solar cells (PSCs). However, a large number of defect states still exist in the PSCs so far and are detrimental to their power conversion efficiencies (PCEs) and stability. Here, an effective strategy of incorporating single-crystalline graphene quantum dots (GQDs) into the perovskite films is proposed to passivate the defect states. Intriguingly, the GQD-modified perovskite films exhibit purer phase structure, higher quality of morphology, and higher electrical conductivity when compared with the control perovskite films. All of the advantages caused by the incorporation of the GQDs lead to fast carrier separation and transport, long carrier lifetime, and low nonradiative recombination in the PSCs based on the GQD-modified perovskite films. As a result, this kind of PSC displays an increase in all photovoltaic parameters, and its PCE shows an enhancement of more than 20% when compared with the control PSC. Moreover, this novel PSC is demonstrated to have long-term stability and resistibility against heat and moisture. Our findings provide an insight into how to passivate the defect states and enhance the electrical conductivities in the perovskites and pave the way for their further exploration to achieve higher photovoltaic performances.
Renoprotection and Its Mechanism of Fasudil in Nitric Oxide Synthase-Deficient Hypertensive Rats
Authors: Zou Wen-bo , Su Jin-zi , Cai Wen-qin , Fan Hou-qiong , Du Feng-ling , Chen Bai-dan 
Published: October 2022

Abstract

Background
To investigate whether fasudil can improve renal microcirculation and protect the kidney in NG-nitro-l-arginine methyl ester (l-NAME)-induced hypertensive rats by inhibiting Rho/Rho associated coiled-coil containing protein kinase (ROCK) signal pathway.

Methods
The nitric oxide-deficient hypertension was induced by l-NAME (60 mg/l·d) which was provided in drinking water for 8 weeks in Wistar rats. Then they were randomly divided into l-NAME and l-NAME + fasudil groups. Blood, urine, and left kidney samples were collected after fasudil intervention for 6 weeks. Renal artery blood flow, renal function markers in serum and urine, morphological changes of renal interlobular artery, and expression levels of related proteins were detected.

Results
Compared with normal control rats, the levels of serum creatinine (SCr) and blood urea nitrogen (BUN) increased while creatinine clearance (CCr) decreased in l-NAME rats. Fasudil treatment significantly decreased SCr and BUN, and increased CCr compared with l-NAME group. Compared with normal controls, the intima of renal interlobular artery increased, the lumen narrowed, the expression of ROCK-1, phosphorylated myosin phosphatase 1/myosin phosphatase 1 (p-MYPT1/MYPT1) increased while endothelial nitric oxide synthase (eNOS) protein levels decreased in l-NAME group (all P &lt; 0.05). Fasudil treatment reduced intimal hyperplasia and lumen stenosis of renal interlobular artery, downregulated ROCK-1 and p-MYPT protein levels and upregulated eNOS expression in l-NAME rats (all P &lt; 0.05).

Conclusions
Fasudil treatment improves renal function and structure of renal interlobar artery in nitric oxide-deficient hypertensive rats induced by l-NAME.
Human Immunodeficiency Virus and Cardiac End-Organ Damage in Women: Findings From an Echocardiographic Study Across the United States
Authors: Shitole Sanyog G , Lazar Jason M , Taub Cynthia C , Furlani Andrea C , Konkle-Parker Deborah J , Dionne-Odom Jodie , Fischl Margaret A , Ofotokun Igho , Adimora Adaora A , Topper Elizabeth F , Golzar Yasmeen , Kassaye Seble G , Gustafson Deborah , Anastos Kathryn , Hanna David B , Xue Xiaonan , Tien Phyllis C , Kaplan Robert C , Kizer Jorge R 
Published: October 2022

Abstract

Background
People with human immunodeficiency virus (HIV) have been reported to have increased risk of clinical and subclinical cardiovascular disease. Existing studies have focused on men and often have been uncontrolled or lacked adequate HIV-negative comparators.

Methods
We performed echocardiography in the Women's Interagency HIV Study to investigate associations of HIV and HIV-specific factors with cardiac phenotypes, including left ventricular systolic dysfunction (LVSD), isolated LV diastolic dysfunction (LVDD), left atrial enlargement (LAE), LV hypertrophy (LVH), and increased tricuspid regurgitation velocity (TRV).

Results
Of 1654 participants (age 51 ± 9 years), 70% had HIV. Sixty-three (5.4%) women with HIV (WWH) had LVSD; 71 (6.5%) had isolated LVDD. Compared with women without HIV (WWOH), WWH had a near-significantly increased risk of LVSD (adjusted relative risk = 1.69; 95% confidence interval = 1.00 to 2.86; P = .051). No significant association was noted for HIV seropositivity with other phenotypes, but there was a risk gradient for decreasing CD4+ count among WWH that approached or reached significance for isolated LVDD, LAE, and LVH. WWH with CD4+ count &lt;200 cells/mm3 had significantly higher prevalence of LAE, LVH, and high TRV than WWOH. There were no consistent associations for viral suppression or antiretroviral drug exposure.

Conclusions
This study suggests that WWH have a higher risk of LVSD compared with sociodemographically similar WWOH, but their risk for isolated LVDD, LAE, LVH, and high TRV is increased only with reduced CD4+ count. Although these findings warrant replication, they support the importance of cardiovascular risk-factor and HIV-disease control for heart disease prevention in this population.
Booster Vaccination Against SARS-CoV-2 Induces Potent Immune Responses in People With Human Immunodeficiency Virus
Authors: Fidler Sarah , Fox Julie , Tipoe Timothy , Longet Stephanie , Tipton Tom , Abeywickrema Movin , Adele Sandra , Alagaratnam Jasmini , Ali Mohammad , Aley Parvinder K , Aslam Suhail , Balasubramanian Anbhu , Bara Anna , Bawa Tanveer , Brown Anthony , Brown Helen , Cappuccini Federica , Davies Sophie , Fowler Jamie , Godfrey Leila , Goodman Anna L , Hilario Kathrine , Hackstein Carl-Philipp , Mathew Moncy , Mujadidi Yama F , Packham Alice , Petersen Claire , Plested Emma , Pollock Katrina M , Ramasamy Maheshi N , Robinson Hannah , Robinson Nicola , Rongkard Patpong , Sanders Helen , Serafimova Teona , Spence Niamh , Waters Anele , Woods Danielle , Zacharopoulou Panagiota , Barnes Eleanor , Dunachie Susanna , Goulder Philip , Klenerman Paul , Winston Alan , Hill Adrian V S , Gilbert Sarah C , Carroll Miles , Pollard Andrew J , Lambe Teresa , Ogbe Ane , Frater John 
Published: October 2022

Abstract

Background
People with human immunodeficiency virus (HIV) on antiretroviral therapy (ART) with good CD4 T-cell counts make effective immune responses following vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are few data on longer term responses and the impact of a booster dose.

Methods
Adults with HIV were enrolled into a single arm open label study. Two doses of ChAdOx1 nCoV-19 were followed 12 months later by a third heterologous vaccine dose. Participants had undetectable viraemia on ART and CD4 counts &gt;350 cells/µL. Immune responses to the ancestral strain and variants of concern were measured by anti-spike immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA), MesoScale Discovery (MSD) anti-spike platform, ACE-2 inhibition, activation induced marker (AIM) assay, and T-cell proliferation.

Findings
In total, 54 participants received 2 doses of ChAdOx1 nCoV-19. 43 received a third dose (42 with BNT162b2; 1 with mRNA-1273) 1 year after the first dose. After the third dose, total anti-SARS-CoV-2 spike IgG titers (MSD), ACE-2 inhibition, and IgG ELISA results were significantly higher compared to Day 182 titers (P &lt; .0001 for all 3). SARS-CoV-2 specific CD4+ T-cell responses measured by AIM against SARS-CoV-2 S1 and S2 peptide pools were significantly increased after a third vaccine compared to 6 months after a first dose, with significant increases in proliferative CD4+ and CD8+ T-cell responses to SARS-CoV-2 S1 and S2 after boosting. Responses to Alpha, Beta, Gamma, and Delta variants were boosted, although to a lesser extent for Omicron.

Conclusions
In PWH receiving a third vaccine dose, there were significant increases in B- and T-cell immunity, including to known variants of concern (VOCs).
Rapid Selection of Sotrovimab Escape Variants in Severe Acute Respiratory Syndrome Coronavirus 2 Omicron-Infected Immunocompromised Patients
Authors: Gliga Smaranda , Lübke Nadine , Killer Alexander , Gruell Henning , Walker Andreas , Dilthey Alexander T , Thielen Alexander , Lohr Carolin , Flaßhove Charlotte , Krieg Sarah , Pereira Joanna Ventura , Seraphin Tobias Paul , Zaufel Alex , Däumer Martin , Orth Hans-Martin , Feldt Torsten , Bode Johannes G , Klein Florian , Timm Jörg , Luedde Tom , Jensen Björn-Erik Ole 
Published: October 2022

Abstract

Background
Monoclonal antibodies (mAbs) that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are predominantly less effective against Omicron variants. Immunocompromised patients often experience prolonged viral shedding, resulting in an increased risk of viral escape.

Methods
In an observational, prospective cohort, 57 patients infected with Omicron variants who received sotrovimab alone or in combination with remdesivir were followed. The study end points were a decrease in SARS-CoV-2 RNA &lt;106 copies/mL in nasopharyngeal swabs at day 21 and the emergence of escape mutations at days 7, 14, and 21 after sotrovimab administration. All SARS-CoV-2 samples were analyzed using whole-genome sequencing. Individual variants within the quasispecies were subsequently quantified and further characterized using a pseudovirus neutralization assay.

Results
The majority of patients (43 of 57, 75.4%) were immunodeficient, predominantly due to immunosuppression after organ transplantation or hematologic malignancies. Infections by Omicron/BA.1 comprised 82.5%, while 17.5% were infected by Omicron/BA.2. Twenty-one days after sotrovimab administration, 12 of 43 (27.9%) immunodeficient patients had prolonged viral shedding compared with 1 of 14 (7.1%) immunocompetent patients (P = .011). Viral spike protein mutations, some specific for Omicron (e.g., P337S and/or E340D/V), emerged in 14 of 43 (32.6%) immunodeficient patients, substantially reducing sensitivity to sotrovimab in a pseudovirus neutralization assay. Combination therapy with remdesivir significantly reduced emergence of escape variants.

Conclusions
Immunocompromised patients face a considerable risk of prolonged viral shedding and emergence of escape mutations after early therapy with sotrovimab. These findings underscore the importance of careful monitoring and the need for dedicated clinical trials in this patient population.
Clinical Presentation, Treatment Response, and Virology Outcomes of Women Who Seroconverted in the Dapivirine Vaginal Ring Trials—The Ring Study and DREAM
Authors: Steytler John , van der Ryst Elna , Craig Charles , Van Baelen Ben , Nuttall Jeremy , van Niekerk Neliëtte , Mellors John , Parikh Urvi , Wallis Carole ,   for the IPM 007 Study Team
Published: October 2022

Abstract

Background
Participants with human immunodeficiency virus (HIV) seroconversion in The Ring Study, a phase 3 trial of dapivirine vaginal ring (DVR), or in the open-label extension trial dapivirine ring extended access and monitoring (DREAM) were offered enrollment in an observational cohort study (IPM 007) to assess clinical presentation and response to antiretroviral therapy (ART).

Methods
Participants’ HIV infection was managed at local treatment clinics according to national treatment guidelines. IPM 007 study visits occurred 3 and 6 months after enrollment and every 6 months thereafter. Assessments included plasma HIV-1 RNA, CD4+ T-cell counts, and recording of HIV/AIDS-associated events and antiretroviral use. Post hoc virology analyses were performed for participants identified with virologic failure.

Results
One hundred fifty-one of 179 eligible participants (84.4%) enrolled into IPM 007; 103 had previously received the DVR in the Ring or DREAM studies, and 48 had received placebo in The Ring Study. HIV-1 RNA and CD4+ T-cell counts after 12 months’ follow-up were similar for participants who used the DVR in The Ring Study and DREAM, compared to those who received placebo. Of the 78 participants with a study visit approximately 6 months after ART initiation, 59 (75.6%) had HIV-1 RNA &lt;40 copies/mL (The Ring Study: placebo: 13/23 [56.5%]; DVR: 32/39 [82.1%]; DREAM [DVR]: 14/16 [87.5%]). Post hoc virology analysis indicated that genotypic patterns observed at virologic failure were as expected of a nonnucleoside reverse transcriptase inhibitor (NNRTI)–based regimen.

Conclusions
Seroconversion during DVR use did not negatively affect clinical presentation or treatment outcome. Mutation patterns at virologic failure were in line with individuals failing an NNRTI-based regimen.

Clinical Trials Registration
NCT01618058.
Development of a Core Outcome Set for Real-world Data in Inflammatory Bowel Disease: A European Crohn’s and Colitis Organisation [ECCO] Position Paper
Authors: Hanzel Jurij , Bossuyt Peter , Pittet Valerie , Samaan Mark , Tripathi Monika , Czuber-Dochan Wladyslawa , Burisch Johan , Leone Salvatore , Saldaña Roberto , Baert Filip , Kopylov Uri , Jäghult Susanna , Adamina Michel , Arebi Naila , Gecse Krisztina 
Published: October 2022

AbstractBackground and AimsThe utility of real-world data is dependent on the quality and homogeneity of reporting. We aimed to develop a core outcome set for real-world studies in adult patients with inflammatory bowel disease [IBD].MethodsCandidate outcomes and outcome measures were identified and categorised in a systematic review. An international panel including patients, dietitians, epidemiologists, gastroenterologists, nurses, pathologists, radiologists, and surgeons participated in a modified Delphi consensus process. A consensus meeting was held to ratify the final core outcome set.ResultsA total of 26 panellists from 13 countries participated in the consensus process. A total of 271 items [130 outcomes, 141 outcome measures] in nine study domains were included in the first-round survey. Panellists agreed that real-world studies on disease activity should report clinical, endoscopic, and biomarker disease activity. A disease-specific clinical index [Harvey–Bradshaw Index, Partial Mayo Score, Simple Clinical Colitis Activity Index] should be used, rather than physician global assessment. In ulcerative colitis [UC], either the UC Endoscopic Index of Severity or the Mayo Endoscopic Score can be used, but there was no consensus on an endoscopic index for Crohn’s disease, nor was there consensus on the use of the presence of ulcers. There was consensus on using faecal calprotectin and C-reactive protein. There was no consensus on the use of histology in real-world studies.ConclusionsA core outcome set for real-world studies in IBD has been developed based on international multidisciplinary consensus. Its adoption will facilitate synthesis in the generation of real-world evidence.
Home monitoring of arterial pulse-wave velocity during COVID-19 total or partial lockdown using connected smart scales
Authors: Bruno Rosa Maria , Pépin Jean Louis , Empana Jean Philippe , Yang Rui Yi , Vercamer Vincent , Jouhaud Paul , Escourrou Pierre , Boutouyrie Pierre 
Published: October 2022

Abstract

Aims
To investigate the impact of coronavirus disease 2019 lockdown on trajectories of arterial pulse-wave velocity in a large population of users of connected smart scales that provide reliable measurements of pulse-wave velocity.

Methods and results
Pulse-wave velocity recordings obtained by Withings Heart Health & Body Composition Wi-Fi Smart Scale users before and during lockdown were analysed. We compared two demonstrative countries: France, where strict lockdown rules were enforced (n = 26 196) and Germany, where lockdown was partial (n = 26 847). Subgroup analysis was conducted in users of activity trackers and home blood pressure monitors. Linear growth curve modelling and trajectory clustering analyses were performed. During lockdown, a significant reduction in vascular stiffness, weight, blood pressure, and physical activity was observed in the overall population. Pulse-wave velocity reduction was greater in France than in Germany, corresponding to 5.2 month reduction in vascular age. In the French population, three clusters of stiffness trajectories were identified: decreasing (21.1%), stable (60.6%), and increasing pulse-wave velocity clusters (18.2%). Decreasing and increasing clusters both had higher pulse-wave velocity and vascular age before lockdown compared with the stable cluster. Only the decreasing cluster showed a significant weight reduction (−400 g), whereas living alone was associated with increasing pulse-wave velocity cluster. No clusters were identified in the German population.

Conclusions
During total lockdown in France, a reduction in pulse-wave velocity in a significant proportion of French users of connected smart bathroom scales occurred. The impact on long-term cardiovascular health remains to be established.
Trends in Frailty Between 1990 and 2020 in Sweden Among 75-, 85-, and 95-Year-Old Women and Men: A Nationwide Study from Sweden
Authors: Wennberg Alexandra M , Ebeling Marcus , Ek Stina , Meyer Anna , Ding Mozhu , Talbäck Mats , Modig Karin 
Published: October 2022

AbstractBackgroundAging is the primary risk factor for frailty, which is defined as an inability to respond to acute or chronic stressors. Individuals are living longer with greater multimorbidity, but there is a paucity of evidence examining frailty across birth cohorts and ages.MethodsWe investigated frailty prevalence and its association with mortality at ages 75, 85, and 95 in the 1895–1945 birth cohorts in Sweden with data from population registries. Frailty was assessed with the Hospital Frailty Risk Score (HFRS).ResultsWe observed that frailty increased with increasing age and that it has become more common in more recent birth cohorts. At age 75, the percent frail in the Total Population Register increased from 1.1% to 4.6% from birth cohorts 1915–1945, corresponding to calendar years 1990–2020. At age 85, the percentage of frail increased from 3.5% to 11.5% from birth cohorts 1905–1935, and at age 95 from birth cohorts 1895–1925, from 4.7% to 18.7%. Our results show that the increase was primarily driven by an increase in the distribution of individuals with scores in the highest quartile of HFRS, while the bottom 3 quartiles remained relatively stable across birth cohorts. Women accounted for a greater distribution of the overall population and frail population, though these disparities decreased over time. Despite increasing levels of frailty, the relationship between frailty and mortality did not change over time, nor did it differ by sex.ConclusionIncreased frailty with improved survival points to a chronic condition that could be intervened upon.