bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human papillomavirus (HPV) genotypes and associated cervical disease in an anti-retroviral setting in Accra, Ghana
Authors: Amelor Dodzi Kofi , Donkoh Emmanuel Timmy , Asmah Richard Harry , Nortey Priscilla , Oppong Samuel Antwi , Wiredu Edwin K 
Published: February 2022

Abstract
Background
The vast majority of women diagnosed with HIV/AIDS are found in the Sub-Saharan African region. These women have a high chance of being infected with human papillomaviruses (HPV), which causes cervical cancer and precursor lesions. Early initiation of HAART coupled with a high HAART compliance may reduce disease burden, but in Ghana, little is known about the distribution of HPV infections and epithelial changes in this vulnerable group.
Methods
This work was carried out to establish the distribution of genital HPV genotypes among women living with HIV attending a special HIV outpatient clinic at the Korle-Bu Teaching hospital Accra, Ghana. Pap smears were performed for 538 selected women. A highly sensitive nested multiplex PCR (NMPCR) assay was conducted for the detection and typing of human papillomavirus (HPV) genotypes. These included, 6/11, 16,18, 31, 33, 35, 39, 42, 43, 44, 45, 51, 52, 56, 58, 59, 66, and 68. Cervical smears were examined for cytologic abnormalities by two cytologists and verified by a pathologist.
Results
Coverage of HAART in this population was 84%. HPV DNA was detected in 280 out of the 538 individuals studied, 52.0% (95%CI 47.7–56.3). Out of these 129 (46.1%, 95%CI 40.1–52.1) had multiple HPV infections and 151 (53.9%, 95%CI 47.9–59.9) had single infections. The prevalence of LR HPV was 10.2% (95% CI: 11.3–17.6). while that of HR HPV was 29.7% (95% CI: 27.4–35.7). The commonest HR types were, 35 ,18 ,58 ,52 and 45 in descending order. The frequency of HPV 16 was 2.4%. Cytologically, 2.8% had ASCUS, 3.9% LGSIL and 2.8% HGSIL, none of the women was found to have atypical glandular cells or adenocarcinoma. The commonest HPV genotypes detected among women with ASCUS were HPV-18 (25% of all ASCUS cases), 52 (25% of all ASCUS cases) and 68 (25% of all ASCUS cases). Among women with LSIL most prevalent were HPV-52 (66.5% of all LSIL cases), HPV-18 (22.2% of all LSIL cases) and HPV 45 (22.2% of all LSIL cases). HPV-16, 52 and 42 were each found in 50% of all High-grade lesions., being the top three in that order for high grade intraepithelial/severe dysplasia lesions
Conclusions
There is a high burden of HPV infection in women living with HIV attending clinic at the KBTH. Given the high prevalence of HIV-HPV coinfection despite the high coverage of HAART, associated cervical lesions represent a major public health burden. These results show that currently available prophylactic vaccines have the potential to be useful in the primary prevention of HPV infections among immunocompromised women. This study also found a cross-sectional association between early age at first sex and the presence of precancerous cervical lesions. Efforts to make vaccines available to young girls before sexual debut should be prioritized along with education on safe sexual habits.
Extracting high-order cosmological information in galaxy surveys with power spectra
Authors: Wang Yuting , Zhao Gong-Bo , Koyama Kazuya , Percival Will , Takahashi Ryuichi , Hikage Chiaki , Gil-Marin Hector , Hahn ChangHoon , Zhao Ruiyang , Zhang Weibing , Mu Xiaoyong , Yu Yu , Zhu Hongming , Ge Fei 
Published: February 2022

Abstract
The "reconstruction" method was proposed more than a decade ago to boost the signal of baryonic acoustic oscillations measured in galaxy redshift surveys, which is one of key probes for dark energy. After moving observed galaxies in galaxy surveys back to their initial position, the reconstructed density field is closer to a linear Gaussian field, with higher-order information moved back into the power spectrum. By combining power spectra measured from the pre- and post-reconstructed galaxy samples, higher-order information beyond the 2-point power spectrum can be efficiently extracted, as power spectra can be measured more quickly than direct measurements of the bispectrum and other higher order functions. This opens a new window to easily use higher-order information when constraining cosmological models.
A Comparison of Explainable Artificial Intelligence Methods in the Phase Classification of Multi-Principal Element Alloys
Authors: Lee Kyungtae , Ayyasamy Mukil V. , Ji Yangfeng , Balachandran Prasanna V. 
Published: February 2022

Abstract
We demonstrate the capabilities of two model-agnostic local post hoc model interpretability methods, namely breakDown (BD) and shapley (SHAP), to explain the predictions of a black-box classification learning model that establishes a quantitative relationship between chemical composition and multi-principal element alloys phase formation. We trained an ensemble of support vector machines using a dataset with 1,821 instances, 12 features with low pair-wise correlation, and seven phase labels. Feature contributions to the model prediction are computed by BD and SHAP for each composition. The resulting BD and SHAP transformed data are then used as inputs to identify similar composition groups using k-means clustering. Explanation-of-clusters by features reveal that the results from SHAP agree more closely with the literature. Visualization of compositions within a cluster using Ceteris-Paribus (CP) profile plots show the functional dependencies between the feature values and predicted response. Despite the differences between BD and SHAP in variable attribution, only minor changes were observed in the CP profile plots. Explanation-of-clusters by examples show that the clusters that share a common phase label contain similar compositions, which clarifies the similar-looking CP profile trends. In the limits of a dataset with independent and non-interacting features, SHAP and BD appear to capture similar pattern.
Genome-wide Analysis of R2R3-MYB Transcription Factors in Boehmeria nivea (L.) Gaudich Revealed Potential Cadmium Tolerance and Anthocyanin Biosynthesis Genes
Authors: Feng Xinkang , Abubakar Aminu Shehu , Chen Kunmei , Yu Chunming , Zhu Aiguo , Chen Jikang , Gao Gang , Wang Xiaofei , Mou Pan , Chen Ping 
Published: February 2022

Abstract
MYB transcription factor (TFs) are one of the largest families in plants, and involved in many biological processes, including growth and development, metabolism and stress response. The MYB TFs has been extensively studied in various plant species. However, comprehensive information on MYB TFs in fiber crop ramie are still unknown. In the current study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. The quantitative real-time qRT-PCR and phylogenetic analysis indicated that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. In conclusion, the studies increase our understanding of the functional roles of MYBs and provided valuable foundation for study of structural and regulatory genes in ramie.
Nanoparticles as Powerful Tools for Crossing the Blood-brain Barrier
Authors: Kazemi-Lomedasht Fatemeh , Hasannejad-Asl Behnam , Pooresmaeil Farkhondeh , Choupani Edris , Dabiri Mehran , Behmardi Abtin , Fadaie Mahmood , Fathi Majid , Moosavi Seyed Akbar , Takamoli Shahla , Hemati Ehsan , Naei Vahid Yaghoubi 
Published: February 2022

Abstract:
The blood-brain barrier (BBB) is considered an important protective barrier in the central
nervous system (CNS). The barrier is mainly formed by endothelial cells (ECs) interconnected by various
junctions such as tight junctions (TJs), gap junctions, and adherent junctions. They collectively
constitute an intensive barrier to the transit of different substances into the brain, selectively permitting
small molecules to pass through by passive movement but holding off large ones such as peptides and
proteins to cross the brain. Hence some molecules selectively transfer across the BBB by active routes
via transcytosis. The BBB also forms a barrier against neurotoxins as well as pathogenic agents. Although
various CNS disorders like Alzheimer's disease (AD) and Parkinson's disease (PD) could hamper
the integrity of the border. Nevertheless, the BBB acts as a barrier for CNS disorders treatment because
it prevents the drugs from reaching their target in the CNS. In recent years, different strategies,
including osmotic disruption of BBB or chemical modification of drugs, have been used to transfer the
chemotherapeutic agents into brain substances. Nowadays, nanoparticles (NPs) have been used as an
effective and non-invasive tool for drug delivery and diagnosis of CNS disorders. In this review, we
discuss the structural characteristic of BBB, safe passageways to cross the BBB, and the relation of
barrier lesions with different CNS disorders. In the end, we explore the progress in drug delivery,
diagnosis, imaging, and treatment of CNS disorders using nanoparticles.
Gut Microbiota Modulation for Therapeutic Management of Various Diseases:
A New Perspective Using Stem Cell Therapy
Authors: Ahmed Lamiaa A. , Al-Massri Khaled F. 
Published: February 2022

Abstract:
Dysbiosis has been linked to various diseases ranging from cardiovascular, neurologic, gastro-intestinal, respiratory, and metabolic illnesses to cancer. Restoring of gut microbiota balance represents an outstanding clinical target for the management of various multidrug-resistant diseases. Preservation of gut microbial diversity and composition could also improve stem cell therapy which now has diverse clinical applications in the field of regenerative medicine.
Gut microbiota modulation and stem cell therapy may be considered a highly promising field that could add up towards the improvement of different diseases, increasing the outcome and efficacy of each other through mutual interplay or interaction between both therapies. Importantly, more investigations are required to reveal the cross‐talk between microbiota modulation and stem cell therapy to pave the way for the development of new therapies with enhanced therapeutic outcomes.
This review provides an overview of dysbiosis in various diseases and their management. It also dis-cusses microbiota modulation via antibiotics, probiotics, prebiotics, and fecal microbiota transplant to introduce the concept of dysbiosis correction for the management of various diseases. Furthermore, we demonstrate the beneficial interactions between microbiota modulation and stem cell therapy as a way for the development of new therapies in addition to limitations and future challenges regarding the applica-tions of these therapies.
Ethnomedicinal Plants Used for Treatment of Urolithiasis in India: A
Review
Authors: Beldar Vishal Gokul , Sidat Parin Salim , Jadhao Manojkumar M. 
Published: February 2022

Background:
Kidney stone is the most commonly observed and painful disease of the
urinary tract in human beings. Numerous intrinsic and extrinsic factors are responsible for the formation
of kidney stones, for instance, age, sex, heredity (intrinsic factors), climate, diet, geography,
mineral composition, and water intake (extrinsic factors). The kidney stones are categorized into
calcium, struvite or magnesium ammonium phosphate, uric acid or urate, cystine, and other types of
stones based on chemical composition and pathogenesis. Due to the multifactorial nature of kidney
stone disease, the patient may need to rely on complex synthetic medication. However, in ancient
Indian history, there are several pieces of evidence where natural resources such as plants were used
to remediation this lethal disease.

Objective:
The present review attempts to provide exhaustive ethnomedicinal and ethnopharmacological
information on medicinal plants used for kidney stones in India.

Result:
Hitherto, 258 ethnomedicinal plants from 90 different families reported using for kidney
stone application. The majority of the plant species are associated with three important families:
Asteraceae, Amaranthaceae, and Fabaceae. Most of the plants are from Andhra Pradesh (43 plants),
followed by East Bengal (38), Jammu & Kashmir (36), Uttarakhand (31), Panjab (27), Mizoram
(23), Karnataka (20), Maharashtra (20) and Assam (18). The commonly used plant parts for the
herbal preparation are roots (21.22 %) followed by leaves/leaf (20.15 %), and sometimes complete
plant (17.77 %) is used. The most commonly used method for the formulation is decoction (46.41
%) followed by powder (18.66 %) and then extracts (15.78 %) of different aerial and non-aerial
parts of the plant. More than sixty ethnomedicinal plants assessed the in-vitro and in-vivo activities
against the kidney stone.

Conclusion:
The present review epitomizes the ethnomedicinal information of medicinal plants
used for kidney stones and pharmacological evidence for anti-urolithiasis activity. Most reported
medicinal plants are not yet scientifically explored and need immediate attention before losing important
species due to excessive deforestation for farming and industrial needs.
The Impact of Long COVID-19 on Mental Health: Observational 6-Month Follow-Up Study
Authors: Houben-Wilke Sarah , Goërtz Yvonne MJ , Delbressine Jeannet M , Vaes Anouk W , Meys Roy , Machado Felipe VC , van Herck Maarten , Burtin Chris , Posthuma Rein , Franssen Frits ME , Vijlbrief Herman , Spies Yvonne , van 't Hul Alex J , Spruit Martijn A , Janssen Daisy JA 
Published: February 2022

Background
The psychological impact of COVID-19 can be substantial. However, knowledge about long-term psychological outcomes in patients with COVID-19 is scarce.

Objective
In this longitudinal, observational study, we aimed to reveal symptoms of posttraumatic stress disorder (PTSD) and symptoms of anxiety and depression up to 6 months after the onset of COVID-19–related symptoms in patients with confirmed COVID-19 and persistent complaints. To demonstrate the impact in nonhospitalized patients, we further aimed to compare these outcomes between nonhospitalized and hospitalized patients.

Methods
Demographics, symptoms of PTSD (Trauma Screening Questionnaire [TSQ] ≥6 points) and symptoms of anxiety and depression (Hospital Anxiety and Depression Scale [HADS] ≥8 points) were assessed at 3 and 6 months after the onset of COVID-19–related symptoms in members of online long COVID-19 peer support groups.

Results
Data from 239 patients with confirmed COVID-19 (198/239, 82.8% female; median age: 50 [IQR 39-56] years) were analyzed. At the 3-month follow-up, 37.2% (89/239) of the patients had symptoms of PTSD, 35.6% (85/239) had symptoms of anxiety, and 46.9% (112/239) had symptoms of depression, which remained high at the 6-month follow-up (64/239, 26.8%, P=.001; 83/239, 34.7%, P=.90; 97/239, 40.6%, P=.08, respectively; versus the 3-month follow-up). TSQ scores and HADS anxiety and depression scores were strongly correlated at the 3- and 6-month follow-ups (r=0.63-0.71, P<.001). Symptoms of PTSD, anxiety, and depression were comparable between hospitalized (n=62) and nonhospitalized (n=177) patients.

Conclusions
A substantial percentage of patients with confirmed COVID-19 and persistent complaints reported symptoms of PTSD, anxiety, or depression 3 and 6 months after the onset of COVID-19–related symptoms. The prevalence rates of symptoms of PTSD, anxiety, and depression were comparable between hospitalized and nonhospitalized patients and merely improved over time. Health care professionals need to be aware of these psychological complications and intervene on time in post-COVID-19 patients with persistent complaints.

Trial Registration
Netherlands Trial Register NTR8705; https://www.trialregister.nl/trial/8705.
Teledermatology in German-Speaking Countries: Patients’ and Physicians’ Perspectives
Authors: Greis Christian , Otten Marina , Reinders Patrick 
Published: February 2022

Background
With increasing digitalization and the current pandemic, teledermatology has gained importance in German-speaking countries in recent years. The regulation on remote consultation methods was recently relaxed, allowing for a more widespread introduction of teledermatological health care services.

Objective
The aim of this work is to evaluate a store-and-forward (SAF) teledermatology application from the patients’ and physicians’ perspectives.

Methods
We carried out a noncontrolled user survey of the web-based platform derma2go in the course of the remote consultation by German dermatologists. Through the platform, patients with dermatological requests could obtain expert advice within a few hours after entering their medical history and uploading photographs of their skin lesions.

Results
A total of 1476 (t1) and 361 (t2) patients and 2207 dermatologist ratings were included within the evaluation. A large proportion of participants were satisfied with the application (t1=83.9%; t2=81.2%). Most participants also rated the usability as high (t1=83.0% satisfied) and were satisfied with the response time of the dermatologists (t1=92.0% satisfied). In addition, a large majority agreed with the statement that they trusted the web-based application (t1=90.5%). At t2, 20.0% of those who participated stated that their skin problem had healed; for 49.8% of participants, it had already improved; for 22.0% of participants, it was unchanged; and for 3.5% of participants, skin problems had worsened. For 64.0% of users, the request was completely resolved, and for 24.2% or users, it was partly resolved as result of the consultation. For 79.7% of users, no additional information was needed by the participating dermatologists. From the practitioners’ perspective, 71.2% of all requests were completely resolved and 24.7% were partly resolved.

Conclusions
Our evaluation has shown that SAF applications, exemplified by derma2go, are likely to improve access to dermatological care, with a high patient satisfaction and a high rate of resolved requests, from the patients’ and physicians’ perspectives. In the future, teledermatological SAF applications can represent a supplement to the existing routine care in dermatology. The indications, patient groups, and use cases, for which the application is particularly suitable, will be determined in further studies.
Utilization of Palliative Care for Patients with COVID-19 and Acute Kidney Injury during a COVID-19 Surge
Authors: Scherer Jennifer S. , Qian Yingzhi , Rau Megan E. , Soomro Qandeel H. , Sullivan Ryan , Linton Janelle , Zhong Judy , Chodosh Joshua , Charytan David M. 
Published: February 2022

Background and objectives
AKI is a common complication of coronavirus disease 2019 (COVID-19) and is associated with high mortality. Palliative care, a specialty that supports patients with serious illness, is valuable for these patients but is historically underutilized in AKI. The objectives of this paper are to describe the use of palliative care in patients with AKI and COVID-19 and their subsequent health care utilization.

Design, setting, participants, & measurements
We conducted a retrospective analysis of New York University Langone Health electronic health data of COVID-19 hospitalizations between March 2, 2020 and August 25, 2020. Regression models were used to examine characteristics associated with receiving a palliative care consult.

Results
Among patients with COVID-19 (n=4276; 40%), those with AKI (n=1310; 31%) were more likely than those without AKI (n=2966; 69%) to receive palliative care (AKI without KRT: adjusted odds ratio, 1.81; 95% confidence interval, 1.40 to 2.33; P<0.001; AKI with KRT: adjusted odds ratio, 2.45; 95% confidence interval, 1.52 to 3.97; P<0.001), even after controlling for markers of critical illness (admission to intensive care units, mechanical ventilation, or modified sequential organ failure assessment score); however, consults came significantly later (10 days from admission versus 5 days; P<0.001). Similarly, 66% of patients initiated on KRT received palliative care versus 37% (P<0.001) of those with AKI not receiving KRT, and timing was also later (12 days from admission versus 9 days; P=0.002). Despite greater use of palliative care, patients with AKI had a significantly longer length of stay, more intensive care unit admissions, and more use of mechanical ventilation. Those with AKI did have a higher frequency of discharges to inpatient hospice (6% versus 3%) and change in code status (34% versus 7%) than those without AKI.

Conclusions
Palliative care was utilized more frequently for patients with AKI and COVID-19 than historically reported in AKI. Despite high mortality, consultation occurred late in the hospital course and was not associated with reduced initiation of life-sustaining interventions.

Podcast
This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2022_02_24_CJN11030821.mp3
Kidney Histopathologic Spectrum and Clinical Indicators Associated with MGRS
Authors: Yong Zi-hao , Yu Xiao-juan , Liu Jing-xia , Zhou Fu-de , Wang Su-xia , Zhao Ming-hui 
Published: February 2022

Background and objectives
Patients with monoclonal gammopathy and concomitant kidney diseases are frequently found in clinical practice. Some of them are diagnosed with monoclonal gammopathy of renal significance (MGRS) due to the presence of monoclonal Ig–related kidney injuries. This study aimed to investigate the histopathologic spectrum and clinical characteristics associated with MGRS in a large cohort of patients with monoclonal gammopathy and biopsy-proven kidney diseases from a single Chinese nephrology referral center.

Design, setting, participants, & measurements
Patients who presented with monoclonal gammopathy (monoclonal spike on serum and/or urine immunofixation tests) and underwent kidney biopsy in the Peking University First Hospital from January 1, 1999 to December 31, 2020 were enrolled in this retrospective study. Patients with malignant hematologic diseases were excluded. Clinical and laboratory data were collected from the electronic medical record system. Comparisons of patients with and without MGRS and with and without amyloidosis were performed. The clinical characteristics associated with MGRS were identified using multivariable logistic regression.

Results
A total of 700 patients with monoclonal gammopathy and kidney biopsy were identified. Thirteen patients with repeat kidney biopsies were analyzed separately. For the remaining 687 patients with one kidney biopsy, 261 patients (38%) had MGRS lesions, and the rest (426 patients, 62%) had non-MGRS kidney diseases. Ig-related amyloidosis accounted for the most MGRS cases (n=164, 63%), followed by monoclonal Ig deposition disease (n=23, 9%) and thrombotic microangiopathy (n=22, 8%). In the non-MGRS group, membranous nephropathy was the most common diagnosis (n=171, 40%). In the multivariable logistic regression model, the presence of abnormal serum free light chain ratio, older age, and greater proteinuria were independently associated with MGRS.

Conclusions
Monoclonal Ig amyloidosis is the leading cause of MGRS in Chinese patients with monoclonal gammopathy. The presence of abnormal free light chain ratio, older age, and greater proteinuria were associated with MGRS.