bluuebunny/crossref_metadata_2025 huggingface dataset:
ZnO-based inverted organic solar cells: a comparative analysis of simulation and experimental devices
Authors: Chambaili  , Ahmad Ibrar , Hayat Khizar , Ahmad Ejaz , Ali Nasir , Safeen Kashif , Shah Abdullah , Tirth Vineet , Algahtani Ali , Shah Said Karim
Published: September 2023

ZnO-based Inverted Organic Solar Cells (OSCs) were simulated using the Solar Cell Capacitance Simulator (SCAPS-1D) software. Two different device architectures were employed: single-layer (SL) and trilayer (TL) configurations. In the SL-OSCs, the structure consisted of a P3HT/PCBM blend between ZnO and molybdenum oxide (MoO3) layers. The P3HT/PCBM blend layers were combined with thin layers from donor (P3HT) and acceptor (PCBM) materials for the TL-OSCs. Electrospray deposition (ESD) was utilized to fabricate the OSCs for comparison. The analysis of the results showed that the TL-OSCs exhibited improved device performance and operational stability compared to the SL devices. Simulated efficiencies were 2.85% for TL and 2.25% for SL, whereas experimental OSCs yielded 1.47% (TL) and 0.84% (SL) efficiencies. This increasing trend in TL-OSCs’ performance aligns with existing literature. Furthermore, the TL OSC structures demonstrated good stability at optimum annealing temperatures up to 130 °C. Additionally, the ZnO-based TL devices displayed enhanced ambient stability under continuous 8h illumination compared to SL-OSCs. This improvement can be attributed to the interfacial layer, which aids in separating charge carriers and reducing recombination rates, consequently enhancing overall device efficiency. The stacked layers in TL OSCs may also function as a barrier, inhibiting diffusion and protecting against moisture and oxygen exposure, thereby contributing to improved device stability.
Silver and nickel modified cobalt-zinc nanostructured ferrites for potential applications
Authors: Kumari Nisha , Himanshi  , Jasrotia Rohit , Liu Louis WY , Ahmed Jahangeer , Hossain Aslam , Henaish A M A , Thakur Sourbh , Singh Virender Pratap , Godara Sachin Kumar , Aggarwal Ridhima , Kandwal Abhishek , Sharma Pankaj
Published: September 2023

In this analysis, silver and nickel modified cobalt-zinc nanostructured ferrites, with chemical compositions of Co0.5Zn0.5AgxNiyFe2-x-yO4 (x = 0.0, 0.01, 0.02, 0.03; y = 0.0, 0.02, 0.03, 0.04) were prepared employing sol–gel auto-combustion (SGAC). All samples were inspected for elementary, structural, microstructural, and magnetic traits. The Fd3m space group geometry with pure spinel phase for the produced nanoferrites was shown by Rietveld’s refined X-ray diffraction patterns. Using the Scherrer formula, X-ray diffraction indicated that samples attain a crystallite size (t) of 38-63 (± 0.01) nm. The field emission scanning electron microscopy revealed that grain growth was not uniform but rather agglomerated, of varying shapes and sizes. The vibrational stretching within the metal-oxygen at interstitial sites was confirmed by Fourier-transform infrared spectroscopy, which clearly indicates the creation of Co-Zn spinel nanoferrites. Furthermore, in all the produced samples, five active Raman vibrational modes (Eg, 3T2g, A1g) are present, and all of these are related to the cubic spinel structure. A vibrating sample magnetometer is utilized to examine the magnetic traits of produced magnetic samples, displaying soft magnetic behavior. The Co0.5Zn0.5AgxNiyFe2-x-yO4 (x = 0.00; y = 0.00) sample attains the maximum saturation magnetization (Ms = 64.94 (± 0.001) emu g−1), whereas the maximum coercivity (Hc = 217.33 ± 0.001 Oe) was attained by the Co0.5Zn0.5AgxNiyFe2-x-yO4 (x = 0.03; y = 0.04) sample, respectively. Therefore, due to the magnetic softness and excellent values of magnetic parameters of the integrated samples, it is possible to use them for potential applications such as recording media, switching, multi-layer chip indicators (MLCIs), and power applications.
Photo-response in chemically synthesized ZnSe nanorod for its application as photosensor
Authors: Handique K C , Barman B , Kalita P K
Published: September 2023

Zinc Selenide nanorods with varying concentration have been synthesized through the chemical bath deposition method. Concentration-dependent structural and electronic properties of synthesized ZnSe nanorods have been studied in this work. XRD and HRTEM studies indicate the formation of cubic polycrystalline ZnSe nanostructures. The effect of molar concentration, incident light intensity and wavelength on various parameters of fabricated ZnSe based photodetectors have been studied. The photocurrent and thereby other parameters such as photosensitivity, responsivity, detectivity and electron quantum efficiency are seen to decrease with the increase of Zn ion concentration. To investigate the fundamental nature of the dependency of photocurrent on light intensity, Rose’s model of photoconduction is used and the intensity-photocurrent characteristics exhibit sub linear nature. The parameters of ZnSe based photodetectors are calculated and correlated with molar concentration. The effects of incident light intensity and the wavelength on the photodetector properties of ZnSe photodetector are studied thoroughly in this paper.
Characterization of optical waveguides in Ce3+-doped phosphate glasses formed by He+ion implantation
Authors: Lu Yan , Chen Yang-Zhi , Zhang Liao-Lin , He Quan-Long , Liu Chun-Xiao
Published: September 2023

In this work, the Ce3+-doped phosphate glass is carried out to fabricate the planar waveguides by the 400 keV He+ ion implantation with a dose of 6.0 × 1016 ions cm−2. The dark-mode spectrum of the waveguide at a wavelength of 632.8 nm is obtained by the prism coupling technique. The SRIM 2013 software is used to analyze the energy deposition induced by the ion implantation and the RCM is employed to reconstruct the refractive index profile of the planar waveguide. The end-face coupling technique is applied to the measurement of the propagation mode image of the waveguide at 632.8 nm. The Ce3+-doped phosphate glass waveguide has the potential for an integrated optical device.
The mechanical universe
Authors: Edmunds Mike
Published: September 2023

Mike Edmunds contemplates the power of mechanical models and what they tell us about our understanding of the universe
Who gets left behind by left behind places?
Authors: Connor Dylan S , Berg Aleksander K , Kemeny Tom , Kedron Peter J
Published: September 2023

We document that children growing up in places left behind by today’s economy experience lower levels of social mobility as adults. Using a longitudinal database that tracks over 20,000 places in the USA from 1980 to 2018, we identify two kinds of left behind places: the ‘long-term left behind’ that have struggled over long periods of history; and ‘recently left-behind’ places where conditions have deteriorated. Compared to children of similar baseline household income levels, we find that exposure to left behind places is associated with a 4-percentile reduction in adult income rank. Children fare considerably better when exposed to places where conditions are improving. These outcomes vary across prominent social and spatial categories and are compounded when nearby places are also experiencing hardship. Based on these findings, we argue that left behind places are having ‘scarring effects’ on children that could manifest long into the future, exacerbating the intergenerational challenges faced by low-income households and communities. Improvements in local economic conditions and outmigration to more prosperous places are, therefore, unlikely to be full remedies for the problems created by left behind places.
Type of Home Care—Informal Versus At Least Some Formal—Matters for Recipients’ Perceived Control
Authors: Wylie Molly J , Boerner Kathrin , Miller Edward Alan , Kim Kyungmin , Burr Jeffrey A
Published: September 2023

Background and Objectives

Perceived control is an important psychological resource for middle-aged and older adults. Aging in place may help foster feelings of control, yet many community-dwelling older adults must rely on others—whether family, friends, or professionals—for physical assistance. This study investigated how receiving home care from different sources was associated with two facets of perceived control (mastery and perceived constraints) among adults with varying levels of physical disability.

Research Design and Methods

Data were drawn from the 2012 and 2014 waves of the Health and Retirement Study. Community-dwelling adults aged 50 years and older receiving help for at least one activity of daily living (ADL) impairment (N = 884) reported their relationship to each respective caregiver (formal professional and/or informal family or friend), level of ADL impairment, and ratings of perceived control. Ordinary least squares regression was used to examine the association between type of support and perceived control, as well as the moderating effect of physical disability on that relationship.

Results

Compared to receipt of informal support alone, receiving a combination of formal and informal support was related to perceptions of greater control over one’s life, but only in terms of mastery. The level of one’s ADL impairment did not have a moderating effect on the relationship between support type and perceived control.

Discussion and Implications

Findings suggested that the type of instrumental support adults receive in their home has implications for specific facets of perceived control. These findings can help inform home care program development.
Exploring the Extent of Usability for Augmented Profile Interfaces in Enhancing Conversation Experiences
Authors: Ryu Hyeyoung , Bang Hyeonseok , Hwang Daeun , Kang Younah
Published: September 2023

In this study, we investigated how to design a usable augmented reality (AR) profile conversation assistant focusing on how and which information leads to enhanced conversation experience and satisfaction. We drew on usability practices including user need interviews, information disposition sessions and an experiment comparing the conversation experiences between AR profile usage and non-usage. We provide insights into how to design a user interface that can enhance users' conversation experience and satisfaction compared to existing interfaces, especially in terms of type, quantity and placement of information on the AR profile. The three main design insights are to (1) limit the topics to personal information, recent events, preferences and hobbies; (2) use a text-based card format with emojis and make a clear distinction between preferred and not preferred topics through font size and placement difference; and (3) limit the number of information provision pages to less than four pages; however, we were not able to resolve the problem of the guilt and artificiality users feel in acquiring information about others from the AR profile. Thus, to resolve this problem, we suggest shifting our paradigm from a techno-solutionist perspective to breaking the illusion of the omnipotence of technology.
Naamyam, Creative Music, and Immigrant Act: Meditations on Jon Jang’s Musical Setting of Genny Lim’s “Burial Mound”
Authors: Law Ho Chak
Published: September 2023

Jon Jang, an American composer, bandleader, and activist of Chinese descent, begins his five-movement Island: The Immigrant Suite No. 1 (1995) with a musical setting that is sonically and stylistically unconventional. He introduces a curious adaptation of naamyam (“southern tones”)—a Cantonese genre of narrative singing that originated in the Pearl River Delta in Guangdong—into this musical setting of Genny Lim’s Chinglish poem “Burial Mound” so as to make audible the politics of representation concerning Sinophone Americans of particular ancestries, generations, and immigration histories. Not only does he associate this setting with Chinese laborers of the transcontinental railroad and naamyam in American Chinatowns, he also demonstrates in this setting his embrace of “creative music” as an American framework of cultural performance.
Comparison of wide and narrow gastric conduit in esophageal cancer surgery
Authors: Chen Yi-Wen , Chuang Cheng-Yen , Yang Shyh-Sheng , Shai Sen-Ei , Lee Ming-Ching , Chen Hao-Yun , Lin Chih-Hung
Published: September 2023

Background:

Gastric conduit is most widely used method for esophageal reconstruction. Despite its popularity, certain complications, such as anastomotic leakage and strictures, remain to be resolved. In the present study, we reviewed the outcomes of narrow gastric conduit compared to wide gastric conduit reconstruction.

Methods:

We retrospectively reviewed 493 patients with esophageal cancer who received esophagectomy with reconstruction in Taichung Veteran General Hospital, Taiwan between January 2010 and December 2019. We performed gastric conduit reconstruction with two different methods, narrow gastric conduit made of multistaples (more than four staples) and wide gastric conduit made of two or three staples. Among the 493 patients, 170 patients underwent wide gastric conduit formation and 323 patients underwent narrow gastric conduit. After propensity score matching, 140 patients from each group were matched by 1:1.

Results:

The average anastomotic leakage rate is 80 of 493 (16.23%). The leakage rate, length of hospital stay, intensive care unit (ICU) admission, and ICU stay were significantly lower in the narrow gastric conduit group than in the wide gastric conduit group. The need for postoperation dilatation was significantly higher in wide gastric conduit group (19.41% vs 11.76%,p= 0.0217), and the time to first dilatation was similar in both groups (p= 0.9808). Similar results were observed even after propensity score matching. In univariate analysis, the narrow gastric conduit, circular stapler, video-assisted thoracic surgery, and laparoscopic surgery were associated with a reduced risk of anastomotic leakage. However, these factors are not statistically significant in a multivariate logistic regression analysis.

Conclusion:

The narrow gastric conduit is not inferior to the wide gastric conduit and can be considered an alternative option for gastric conduit preparation.
Favorable effect of herbal extract on androgenic alopecia: A case report
Authors: Qian Yuxin , Zhu Lijian , Wu Lan , Chen Jingya , Ding Bin , Li Yuanyuan , Cao Yi
Published: September 2023

Rationale:

Androgenic alopecia (AGA) is a prevalent condition with progressive miniaturization of hair follicles. Currently, reliable treatments have remained limited, and complementary medications for AGA are still being investigated. Traditional Chinese medicine formulas have conspicuous advantages in the treatment of AGA with good development prospects. Zimmer aqueous spray (ZAS) is a water spray containing Zimmer herbal extract powder (ZMWP), which consists of Ligustri lucidi Fructus, Ecliptae Herba, Fallopia multiflora (Thunb.) Harald. and Polygonatum sibiricum Delar. ex Redoute, etc. ZMWP is an active ingredient in the prevention of hair loss. Our aim is to provide evidence for the effectiveness of ZAS in the treatment of AGA.

Patient concerns:

A 41-year-old man had suffered from hair loss for 8 years.

Interventions:

The patient with moderate AGA received 3 to 4 mL ZAS daily or every other day for 3 months.

Outcomes:

The hair density obviously increased after 3 months of therapy. The improvement of hair diameter, vellus hair rate, and 1 hair pilosebaceous unit rate were observed with a trichoscopy and quantitatively analyzed. Besides, honeycomb pigment pattern mitigated and arborized red lines.

Lessons:

The results suggested that ZMWP might have the capability of improving hair growth and attenuating AGA, which can be a promising alternative treatment of AGA.
The association between short-term exposure to nitrogen dioxide and hospital admission for schizophrenia: A systematic review and meta-analysis
Authors: Xu Jiating , Lan Zhiyong , Xu Penghao , Zhang Zhihua
Published: September 2023

Background:

Ambient air pollution has been identified as a primary risk factor for mental disorders. In recent years, the relationship between exposure to ambient nitrogen dioxide (NO2) and the risk of hospital admissions (HAs) for schizophrenia has garnered increasing scientific interest, but evidence from epidemiological studies has been inconsistent. Therefore, a systematic review and meta-analysis were conducted to comprehensively identify potential correlations.

Methods:

A literature search in 3 international databases was conducted before December 31, 2022. Relative risk (RR) and corresponding 95% confidence intervals (CI) were calculated to evaluate the strength of the associations. Summary effect sizes were calculated using a random-effects model due to the expected heterogeneity (I
2 over 50%).

Results:

A total of ten eligible studies were included in the meta-analysis, including 1,412,860 participants. The pooled analysis found that an increased risk of HAs for schizophrenia was associated with exposure to each increase of 10 μg/m3 in NO2 (RR = 1.029, 95% CI = 1.016–1.041, P < .001). However, the heterogeneity was high for the summary estimates, reducing the credibility of the evidence. In 2-pollutant models, results for NO2 increased by 0.3%, 0.2% and 2.3%, respectively, after adjusting for PM2.5, PM10 and SO2.

Conclusions:

This study provides evidence that NO2 exposure significantly increases the risk of hospital admission for schizophrenia. Future studies are required to clarify the potential biological mechanism between schizophrenia and NO2 exposure to provide a more definitive result.
Lennox-Gastaut syndrome characterized by super-refractory status epilepticus treated with high-dose anesthetics: A case report
Authors: Yang Xiaoqian , Xu Guangjun , Chong Zonglei , Liang Yangyang , Du Jingwei , Zhao Lin , Chen Wei
Published: September 2023

Rationale:

Super-refractory status epilepticus is a serious illness with high morbidity and mortality, which is defined as an SE that continues or recurs 24 hours or more after the onset of anesthesia. Anesthetic agents can be either pro-convulsant or anticonvulsant or both.

Patient concerns:

Epilepsy occurred at the age of 3 years. At the age of 4 years, generalized tonic-clonic seizure occurred for the first time. The patient was hospitalized at the age of 27 and 28 years for treating status epilepticus. At the age of 33 years, antiepileptic drugs were stopped due to poor appetite. In an early morning, the patient was found delirious with reduced speech.

Diagnosis:

Occasionally, the patient blinked his eyelids, or deflected his eyeballs to 1 side. When propofol was lowered to 10 mL/H, the epileptic wave reduced obviously. Afterwards, the patient opened his eyes autonomously and his consciousness gradually recovered. The patient could answer questions, and the limbs had voluntary movements. The patient breathing also gradually recovered, and his urine gradually returned to pale yellow from green. After anesthetic was stopped for 10 days, the patient lost his consciousness again. The patient eyes turned upward frequently, which was relieved in 1 to 2 seconds with an attack once every 2 to 5 minutes.

Interventions:

Clonazepam was gradually reduced to 2 mg qn, and the patient gradually woke up during this process. The patient was also treated with levetiracetam 1.5 g bid, oxcarbazepine 0.6 g bid, topiramate 50 mg bid and valproate 0.4 g tid.

Outcomes:

After 1 month follow-up, status epilepticus did not appear again.

Lessons:

Propofol aggravated the tonic seizures. As tonic seizures occur during natural sleep and after sleep induced by various narcotic drugs, the decrease of consciousness level induced by excessive sedation of narcotic drugs has been suggested as the reason for poor seizure control.
Global trends and future prospects of COVID-19 and physical activity: Bibliometric analysis
Authors: Toktaş Neşe , Köse Elif , Lapa Tennur-Yerlisu , Kaas Evren-Tercan , Serdar Yücel Ali , Derman Süleyman
Published: September 2023

Background:

Containment measures implemented during the COVID-19 pandemic have led to drastic changes in daily life and effects on health behaviors such as decrease in physical activity (PA) levels. This study aims to present a general framework to researchers on COVID-19 and PA research in relation with changes in studies within years, current trend topics, gaps in the research field and possible future trends.

Methods:

A total of 1819 articles indexed in the WoS core collection database were analyzed according to publication year, citation, country and institution collaborations, coword, co-citation networks, concept–topic trends and topic clusters using bibliometric analysis.

Results:

The most productive country was the USA(n = 335), and the most productive institution was University of London in UK (n = 38). The most cited publication was the study by Ammar et al, (2020) (n = 188). In 2020, the most popular topics were PA and health meanwhile in 2021 behavior, lifestyle, social media and in 2022 habits, long COVID, sleep quality topics were in the foreground. Studies in 2023 focus on how COVID-19 affects PA habits and the associations between COVID-19-based anxiety and sleep patterns. These studies focused especially on effects of sport participation on life quality, diet, depression, mental health on young athletes, children, adolescent persons, older adult groups.

Conclusions:

An important gap in the study area is research on effect of changing lifestyle due to pandemic on individuals and the society during the Post COVID-19 period. If benefits of PA will not be limited to only physical benefits and psychological emotional, cognitive and social benefits are also taken into consideration, it is important that researchers conduct long-term and widescale observations.
Efficacy of autogenous tooth block for lateral ridge augmentation compared with autogenous bone block: A systematic review and meta-analysis
Authors: Guan Delin , Zhao Ruimin , Guo Yan , Li Jianxue , Ma Na , Gong Jiaming
Published: September 2023

Background:

Autogenous tooth block (ATB) has been used as an alternative material for bone regeneration, but its efficacy compared with autogenous bone block (ABB) remains uncertain. The aim of this systematic review was to investigate and compare the clinical and histological performance of ATB and ABB grafts in lateral alveolar ridge augmentation (LARA).

Methods:

Electronic retrieval of MEDLINE, Embase, Cochrane Library (CENTRAL), Scopus, Web of Science, China national knowledge infrastructure, Wanfang data, SinoMed, and manual searching until July 2023 were used to identify controlled clinical trials employing ATB grafts in LARA. The identified reports included at least one of the following outcome variables: ridge width gain, graft resorption, postoperative complications, histology, and histomorphometry. Weighted or mean differences (MD), relative risk, and corresponding 95% confidence intervals (CI) were calculated. Descriptive analysis was applied to the qualitative statistics. The protocol followed the preferred reporting items for systematic reviews and meta-analyses statement and was prospectively registered in PROSPERO (CRD42023399611).

Results:

Four controlled clinical trials with 77 participants each using ATB and ABB grafts were included. Meta-analysis indicated that ATB grafts resulted in greater bone width (MD = 1.31, 95% CI [0.92, 1.71], P < .00001) and less graft resorption (MD = −0.71, 95% CI [−1.22, −0.21], P = .005) than ABB grafts on LARA. There was no statistical difference in postoperative complications between ATB and ABB grafts (relative risk = 0.81, 95% CI [0.32, 2.04], P = .66). Furthermore, the ATB grafts exhibited positive replacement resorption with alveolar bone for favorable signs of new bone activity on histology and histomorphometry.

Conclusion:

Within the limitations of this study, ATB grafts could serve as an alternative material for ABB to support LARA. Further research with a longer follow-up period is required to verify these findings.
Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy
Authors: Yuan LinHui , Zhang LiJun , Liu Xin , Li Sheng , Zou JiXin
Published: September 2023

Background:

Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients.

Methods:

In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA—hub genes and transcription factor (TF)—hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments.

Results:

A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference.

Conclusion:

This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization.
Making Sense of the Infant Formula Shortage
Authors: Abrams Steven A.
Published: September 2023

Purchasing infant formula became an enormous challenge beginning in early 2022 for families throughout the United States. Faced with a myriad of other challenges in raising newborns came the unexpected reality of not having food in stores that their infants needed to thrive. Quickly, blame was assessed, and less quickly, government and industry solutions to increase supply were set in motion, but the actions taken have not fully resolved shortages. Even more than a year and a half after the severe shortages began, little effort has been made to develop long-term solutions to formula supply issues. It is time for the nutrition community to seriously consider this issue as a major policy agenda and recognize that healthy childhood nutrition starts with secure feeding for all infants regardless of mode or content of feeding. In this article, we will explore what needs to be done in this regard and where the barriers are to implementing long-term solutions to both the formula shortage and supporting breastfeeding families.
Topical Cream Derived From Hylocereus polyrhizus (Red Dragon Fruit) Extract Accelerates Wound Healing Through Increased Hydroxyproline and Fibroblast Growth Factor 2 Levels: A Pilot Study
Authors: Tahir Takdir , Djamaluddin Nurdiana , Thalib Abdul , Maryunis Maryunis , Yusuf Saldy , Riskayani Fifi , Fitria Fitria
Published: September 2023

The red dragon fruit (Hylocereus polyrhizus) extract (RDFE) is frequently used for a variety of therapeutic purposes (e.g., boosting the immune system, promoting a healthy gastrointestinal system, improving wound healing). We investigated the effects of a topical cream containing 7.5% RDFE on hydroxyproline and fibroblast growth factor 2 (FGF-2) levels and wound healing. On Day 0, we divided a total of 36 albino male Wistar rats into two equal groups. Using an 8-mm punch biopsy, we created a circular excision to fascial depth on the back of each rat. On Day 1, we treated the control group (n = 18) with 20 mg of base cream and the RDFE group (n = 18) with 20 mg of 7.5% RDFE cream. We measured hydroxyproline and FGF-2 levels in the wound tissue using an ELISA method on Days 3, 7, and 14. We found that on Day 3, hydroxyproline levels were significantly lower in the treatment group than in the control group (p = .031). We also found a significant correlation between FGF-2 levels in the treatment group and wound diameter (p = .02). On the basis of the results of this study, we concluded that using a topical cream containing 7.5% RDFE has the potential to accelerate wound healing by increasing levels of hydroxyproline and FGF-2 in the wound.
Immunogenicity of tetanus, diphtheria and acellular pertussis vaccination among pregnant women living with and without HIV
Authors: Nunes Marta C. , Tamblyn Amy , Jose Lisa , Ntsimane Mathapelo , Lerotholi Ntoetse , Machimana Charmaine , Taylor Ashleigh , Laher Farzanah , Madhi Shabir A.
Published: September 2023

Objective:

Vaccination during pregnancy with tetanus–diphtheria–acellular pertussis (Tdap) vaccine is recommended to protect the young infants against pertussis. There is a paucity of data on immune responses to Tdap in pregnant women with HIV (PWWH), and its impact on the protection of their infants has not been described.

Methods:

In an open label phase IV clinical trial in South Africa, we evaluated the immunogenicity and safety of Tdap in PWWH compared with HIV-uninfected women. Antigen-specific immunoglobulin G (IgG) to pertussis toxoid, filamentous haemagglutinin, pertactin, fimbriae, diphtheria and tetanus were measured by electrochemiluminescence-based multiplex assay.

Results:

Overall, 91 PWWH and 136 HIV-uninfected pregnant women were enrolled. All PWWH were on antiretroviral treatment and 94.5% had HIV viral loads <40 copies per millilitre. Antibody levels prevaccination were lower among PWWH compared with HIV-uninfected women for all antigens. At 1 month postvaccination PWWH compared with HIV-uninfected women had lower fold-increase and antibody concentrations for all epitopes. Also, a lower proportion of PWWH achieved ≥4-fold increase from pre to postvaccination for pertussis toxoid and pertactin, or diphtheria IgG levels ≥0.1 IU/ml and ≥1 IU/ml postvaccination. Adverse events postvaccination were similar in PWWH and HIV-uninfected.

Conclusion:

Tdap vaccination was safe and immunogenic. PWHW had, however, attenuated humoral immune responses, which could affect the effectiveness of protecting their infants against pertussis compared with those born to women without HIV.

ClinicalTrials.gov identifier: NCT05264662
Mapping the anatomical and transcriptional landscape of early human fetal ovary development
Authors: McGlacken-Byrne Sinead M , del Valle Ignacio , Xenakis Theodoros , Simcock Ian C , Suntharalingham Jenifer P , Buonocore Federica , Crespo Berta , Moreno Nadjeda , Liptrot Danielle , Niola Paola , Brooks Tony , Conway Gerard S , Dattani Mehul T , Arthurs Owen J , Solanky Nita , Achermann John C
Published: September 2023

The complex genetic mechanisms underlying human ovary development can give rise to clinical phenotypes if disrupted, such as Primary Ovarian Insufficiency and Differences of Sex Development. Through a clinically-focused lens, we combine single-nuclei RNA sequencing, bulk RNA sequencing, and micro-focus computed tomography to elucidate the anatomy and transcriptional landscape of the human fetal ovary across key developmental timepoints (Carnegie Stage 22 until 20 weeks post conception). We show the marked growth and distinct morphological changes within the fetal ovary at the critical timepoint of germ cell expansion, and demonstrate that the fetal ovary becomes more transcriptomically distinct from the testis with age. We describe novel ovary developmental pathways, relating to neuroendocrine signalling, energy homeostasis, mitochondrial networks, piRNA processes, and inflammasome regulation. We define transcriptional regulators and candidate genes for meiosis within the developing ovary. Together, this work advances our fundamental understanding of human ovary development and clinical ovarian insufficiency phenotypes.
A simple method to genetically differentiate invasive F1Typhahybrids (T. ×glauca) and advanced-generation/backcrossed hybrids from parent species (T. latifoliaandT. angustifolia) in eastern Canada and northeastern USA
Authors: Chambers Avery , Chambers Braidy , Bhargava Deven , Aleman Alberto , Dorken Marcel , Freeland Joanna
Published: September 2023

A widespreadTypha(cattail) hybrid zone in southeastern Canada and northeastern USA comprisesT. latifolia, T. angustifolia, and their hybridT. ×glauca. In this region the hybrid is considered invasive because of its detrimental impacts on wetlands and biodiversity. Researchers and managers are increasingly interested in tracking and controlling the spread of the invasive hybrid, but this can be hampered by challenges in differentiating taxa: while the parent species and F1 hybrids can often be identified from morphological characteristics, advanced-generation and backcrossed hybrids can be common, and these have obscured morphological distinctions among taxa. Here we present five species-specific genetic markers that differentiateT. latifolia, T. angustifolia, F1hybrids, and advanced-generation/backcrossed hybrids. Unlike the pre-existing species-specific microsatellite markers, these markers require only PCR or PCR followed by a restriction enzyme digest, and can be visualized on an agarose gel. As a result, they require less specialized equipment than existing species-specific markers, and should therefore be useful for a larger group of practitioners. Future use of these markers could include monitoring range expansions, assessing the outcomes of restoration programs, and avoiding the unnecessary elimination of nativeTypha.
SCancerRNA: Expression at the Single Cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers
Authors: Guo Hongzhe , Zhang Liyuan , Cui Xinran , Cheng Liang , Zhao Tianyi , Wang Yadong
Published: September 2023

Non-coding RNAs (ncRNAs) participate in multiple biological processes associated with cancer as tumor suppressors or oncogenic drivers. Due to their high stability in plasma, urine, and many other fluids, ncRNAs have the potential to serve as key biomarkers for early diagnosis and screening of cancers. During cancer progression, tumor heterogeneity plays a crucial role, and it is particularly important to understand the gene expression patterns of individual cells. With the development of single-cell RNA sequencing (scRNA-seq) technologies, uncovering gene expression in different cell types for human cancers has become feasible by profiling transcriptomes at the cellular level. However, a well-organized and comprehensive online resource that provides access to the expression of genes corresponding to ncRNA biomarkers in different cell types at the single cell level is not available yet. Therefore, we developed the SCancerRNA database to summarize experimentally supported data on long ncRNA (lncRNA), microRNA (miRNA), piwi-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and circular RNA (circRNA) biomarkers, as well as data on their differential expression at the cellular level. Furthermore, we collected biological functions and clinical applications of biomarkers to facilitate the application of ncRNA biomarkers to cancer diagnosis, as well as monitoring of progression and targeted therapies. SCancerRNA also allows users to explore interaction networks of different types of ncRNAs, and build computational models in the future. SCancerRNA is freely accessible athttp://www.scancerrna.com/BioMarker.
Deep Variational Autoencoders for Population Genetics
Authors: Geleta Margarita , Montserrat Daniel Mas , Giro-i-Nieto Xavier , Ioannidis Alexander G.
Published: September 2023

Motivation

Modern biobanks provide numerous high-resolution genomic sequences of diverse populations. These datasets enable a better understanding of genotype-phenotype interactions with genome-wide association studies (GWAS) and power a new personalized precision medicine with polygenic risk scores (PRS). In order to account for diverse and admixed populations, new algorithmic tools are needed in order to properly capture the genetic composition of populations. Here we explore deep learning techniques, namely variational autoencoders (VAEs), to process genomic data from a population perspective. We hope this work will encourage the adoption of deep neural networks in the population genetics community.

Results

In this paper, we show the power of VAEs for a variety of tasks relating to the interpretation, classification, simulation, and compression of genomic data with several worldwide whole genome datasets from both humans and canids and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning of granular population structure and inferring of informative latent factors. The learned latent spaces of VAEs are able to capture and represent differentiated Gaussian-like clusters of samples with similar genetic composition on a fine-scale from single nucleotide polymorphisms (SNPs), enabling applications in dimensionality reduction, data simulation, and imputation. These individual genotype sequences can then be decomposed into latent representations and reconstruction errors (residuals) which provide a sparse representation useful for lossless compression. We show that different population groups have differentiated compression ratios and classification accuracies. Additionally, we analyze the entropy of the SNP data, its effect on compression across populations, its relation to historical migrations, and we show how to introduce autoencoders into existing compression pipelines.
Structure-based humanization of a therapeutic antibody for Multiple Myeloma
Authors: Marino Stephen F. , Daumke Oliver
Published: September 2023

The optimal efficacy of xenogeneically generated proteins intended for application in humans requires that their own antigenicity be minimized. This necessary adaptation of antibodies to a humanized version poses challenges since modifications even distant from the binding sites can greatly influence antigen recognition and this is the primary feature that must be maintained during all modifications. Current strategies often rely on grafting and/or randomization/selection to arrive at a humanized variant retaining the binding properties of the original molecule. However, in terms of speed and efficiency, rationally directed approaches can be superior, provided the requisite structural information is available. We present here a humanization procedure based on the high-resolution X-ray structure of a chimeric IgG against a marker for Multiple Myeloma. Based onin silicomodelling of humanizing amino acid substitutions identified from sequence alignments, we devised a straightforward cloning procedure to rapidly evaluate the proposed sequence changes. Careful inspection of the structure allowed identification of a potentially problematic amino acid change that indeed disrupted antigen binding. Subsequent optimization of the antigen binding loop sequences resulted in substantial recovery of binding affinity lost in the completely humanized antibody. X-ray structures of the humanized and optimized variants demonstrate that the antigen binding mode is preserved, with surprisingly few direct contacts to antibody atoms. These results underline the importance of structural information for the efficient optimization of protein therapeutics.
skDER: microbial genome dereplication approaches for comparative and metagenomic applications
Authors: Salamzade Rauf , Kalan Lindsay R.
Published: September 2023

skDER (https://github.com/raufs/skDER) combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes by skani1with two low-memory methods for genomic dereplication. The first method implements a dynamic algorithm to determine a concise set of representative genomes. This approach is well-suited for selecting reference genomes to align metagenomic reads onto for tracking strain presence across related microbiome samples. This is because fewer representative genomes should alleviate the concern that reads belonging to the same strain get falsely partitioned across closely related genomes. The other method, which uses a greedy approach, is better suited for use in comparative genomics, where users might be overwhelmed with the high number of genomes available for certain taxa and aim to reduce redundancy and, therefore, computational requirements for downstream analytics. This method selects a larger number of representative genomes to comprehensively sample the pangenome space for the taxon of interest. To further aid usage for comparative genomics studies, skDER also features an option to automatically download genomes classified as a particular species or genus in the Genome Taxonomy Database2–4and we provide precomputed representative genomes for commonly studied bacterial taxa5.
PspA-mediated aggregation protectsStreptococcus pneumoniaeagainst desiccation on fomites
Authors: Lane Jessica R. , Tata Muralidhar , Yasmin Rahena , Im Hansol , Briles David E. , Orihuela Carlos J.
Published: September 2023

Streptococcus pneumoniae(Spn) resides in the nasopharynx where it can disseminate to cause disease. One keySpnvirulence factor is pneumococcal surface protein A (PspA), which promotes survival by blocking the antimicrobial peptide lactoferricin. PspA has also been shown to mediate attachment to dying epithelial cells in the lower airway due to its binding of cell surface-bound mammalian (m)GAPDH. Importantly, the role of PspA during colonization is not well understood. WildtypeSpnwas present in nasal lavage elutes collected from asymptomatically colonized mice at levels ∼10-fold higher that its isogenic PspA-deficient mutant (ΔpspA). WildtypeSpnalso formed aggregates in mucosal secretions composed of sloughed epithelial cells and hundreds of pneumococci, whereas ΔpspAdid not.Spnwithin the center of these aggregates better survived prolonged desiccation on fomites than individual pneumococci and were capable of infecting naïve mice, indicating PspA-mediated aggregation conferred a survival/transmission advantage. Incubation ofSpnin saline containing mGAPDH also enhanced tolerance to desiccation, but only for wildtypeSpn. mGAPDH was sufficient to cause low-level aggregation of wildtypeSpnbut not ΔpspA. In strain WU2, the subdomain of PspA responsible for binding GAPDH (aa230-281) is ensconced within the lactoferrin (LF)-binding domain (aa167-288). We observed that LF inhibited GAPDH-mediated aggregation and desiccation tolerance. Using surface plasmon resonance, we determined thatSpnforms multimeric complexes of PspA-GAPDH-LF on its surface and that LF dislodges GAPDH. Our findings have important implications regarding pneumococcal colonization/transmission processes and ongoing PspA-focused immunization efforts for this deadly pathogen.

IMPORTANCE

Streptococcus pneumoniae(Spn) is a dangerous human pathogen capable of causing pneumonia and invasive disease. The virulence factor pneumococcal surface protein A (PspA) has been studied for nearly four decades with well-established roles in pneumococcal evasion of C-reactive protein and neutralization of lactoferricin. Herein, we show that mammalian (m)GAPDH in mucosal secretions promotes aggregation of pneumococci in a PspA-dependent fashion, whereas lactoferrin counters this effect. PspA-mediated GAPDH-dependent bacterial aggregation protectedSpnin nasal lavage elutes and grownin vitrofrom desiccation on fomites. Furthermore, surviving pneumococci within these aggregates retained their ability to colonize naïve hosts after desiccation. We report thatSpnbinds to and forms protein complexes on its surface composed of PspA, mGAPDH, and lactoferrin. Changes in the levels of these proteins therefore most likely have critical implications onSpncolonization, survival on fomites, and transmission.
Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness
Authors: Odom Aubrey R. , McClintock Jessica , Gill Christopher J. , Pieciak Rachel , Ismail Arshad , MacLeod William B. , Johnson W. Evan , Lapidot Rotem
Published: September 2023

Introduction

Associative connections have previously been identified between nasopharyngeal infections and infant mortality. The nasopharyngeal microbiome may potentially influence the severity of these infections.

Methods

We conducted an analysis of a longitudinal prospective cohort study of 1,981 infants who underwent nasopharyngeal sampling from 1 week through 14 weeks of age at 2–3-week intervals. In all, 27 microbiome samples from 9 of the infants in the cohort who developed fatal acute febrile illness (fAFI) were analyzed in pooled comparisons with 69 samples from 10 healthy comparator infants. We completed 16S rRNA amplicon gene sequencing all infant NP samples and characterized the maturation of the infant NP microbiome among the fAFI(+) and fAFI(-) infant cohorts.

Results

Beta diversity measures of fAFI(-) infants were markedly higher than those of fAFI(+) infants. The fAFI(+) infant NP microbiome was marked by higher abundances ofEscherichia, Pseudomonas, Leuconostoc, andWeissella, with low relative presence ofAlkalibacterium, Dolosigranulum, Moraxella, andStreptococcus.

Conclusions

Our results suggest that nasopharyngeal microbiome dysbiosis precedes fAFI in young infants. Early dysbiosis, involving microbes such asEscherichia, may play a role in the causal pathway leading to fAFI or could be a marker of other pathogenic forces that directly lead to fAFI.
Variable and reversible opacification process on IOLs for cataract simulation
Authors: Akyazi Deniz , Zolfaghari Parviz , Sahin Afsun , Urey Hakan
Published: September 2023

Understanding vision through mild and dense cataracts is important for vision scientists and IOL developers. There have been virtual simulators using VR headsets for subjective evaluation of cataractous vision. However, a physical intraocular lens with variable cataracts for objective evaluation is not available. In this study, we developed a reversible process that can be selectively applied to the whole or parts of an IOL to affect the opacification level. We used our eye model and developed a cataractous lens simulator for progressive levels of opacification, which is achieved by applying a reversible chemical procedure on the intraocular lens surfaces. After the lens is fully or partially immersed in acetone, subsequent testing of the lens in distilled water results in a progressive change in opacification level within minutes. We measured the quality of vision by obtaining modulation transfer function curves, transmission, and spectroscopic measurements at different opacification levels. By simulating variable opacification across the IOLs, we tested how vision changes from less dense to more dense cataractous regions in a holographic display system with programmable small exit pupils. All results were consistent with the expected vision degradation caused by natural opacification.