bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Safety of Solid-state Dual-wavelength Lasers for the Treatment of Moderate-to-severe Inflammatory Acne in Asian Populations
Authors: Lim Joyce Teng-Ee 
Published: January 2024

Background:
Standard treatments for moderate-to-severe acne often require oral medications but are not long-lasting or free from side effects. We aimed to evaluate the efficacy and safety of a solid-state dual-wavelength laser for moderate-to-severe inflammatory acne in an Asian population.

Methods:
Forty individuals with moderate-to-severe acne received nightly topical retinoids and two to three weekly treatments with a 1319-nm laser followed by a 589-nm laser (five sessions in total). Patients were evaluated at pretreatment baseline, at monthly intervals, and at 1 month after the last laser for pain, seborrhea, global aesthetic improvements, and satisfaction, using standardized digital photography and global assessment scales. Fifteen patients had an additional evaluation 3 months after the fifth session.

Results:
At 1 month, all patients (n = 40) had improved inflammatory acne counts, with 72.5% having greater than 75% reduction in acne count, 7.5% having 51%–75% reduction, 17.5% having 26%–50% reduction and 2.5% having less than 25% reduction. Moreover, GAS evaluations showed that 62.5% of patients improved to almost clear and 37.5% to mild acne (P = 0.0478), while improvements were sustained in patients with 3-month follow-ups. Erythema (n = 29) improved with 65.5% of affected patients having greater than 75% reduction. Patients (n = 17) with pigmentation experienced lightening, with 52.9% of affected patients having a greater than 75% reduction. With low pain scores (mean 3.68 of 10, median 4 of 10), the treatment was well-tolerated. All patients (n = 40) reported acne improvements with 95% having much improved or very much improved, and 95% either satisfied or very satisfied.

Conclusions:
Dual-wavelength lasers effectively and safely treat moderate-to-severe inflammatory acne with high patient satisfaction. It is ideal for patients who refuse or are contraindicated to oral medications, and patients with acne-associated pigmentation, erythema and seborrhea.
Phase 2, open-label, rollover study of cenicriviroc for liver fibrosis associated with metabolic dysfunction–associated steatohepatitis
Authors: Francque Sven M. , Hodge Alexander , Boursier Jerome , Younes Ziad H. , Rodriguez-Araujo Gerardo , Park Grace S. , Alkhouri Naim , Abdelmalek Manal F. 
Published: January 2024

Background:
Cenicriviroc (CVC) is a novel, orally administered antagonist of chemokine receptor types 2/5 that has demonstrated antifibrotic activity in a phase 2b study of patients with NASH. This phase 2, open-label, rollover study investigated the long-term safety and tolerability of CVC in patients with NASH and stage 0–4 liver fibrosis.

Methods:
Eligible patients who completed the phase 2 CENTAUR study or reached a predefined endpoint in the phase 3 AURORA study were rolled over and received open-label CVC 150 mg once daily. Safety assessments were conducted at the start of the study, and patients were seen in the clinic every 3 months until the study sponsor terminated CVC development. Safety endpoints included treatment-emergent adverse events (TEAEs), treatment-related TEAEs, adverse event severity, and clinical laboratory assessments.

Results:
A total of 167 patients were enrolled, with a median treatment duration of 33.6 months. Before study termination, 36 patients (21.6%) prematurely discontinued the study. Treatment-related TEAEs were reported in 28 patients (16.8%). The most common treatment-related TEAEs were 4 cases of diarrhea (2.4%) and 2 cases each (1.2%) of abdominal pain, nausea, alanine aminotransferase increased, aspartate aminotransferase increased, hypertriglyceridemia, myalgia, pruritus, and rash. The majority of these treatment-related events were mild in intensity, and none were life-threatening. There were no clinically meaningful changes in hepatic function, chemistry, or liver parameters from baseline to the end of the study.

Conclusions:
In this rollover study, CVC 150 mg once daily was well tolerated in patients with NASH and stage 0–4 liver fibrosis. No new safety signals were reported, and these data further support the safety and tolerability of CVC.
Granulocyte-monocyte/macrophage apheresis for steroid-nonresponsive or steroid-intolerant severe alcohol-associated hepatitis: A pilot study
Authors: Kasuga Ryosuke , Chu Po-sung , Taniki Nobuhito , Yoshida Aya , Morikawa Rei , Tabuchi Takaya , Noguchi Fumie , Yamataka Karin , Nakadai Yukie , Kondo Mayuko , Ebinuma Hirotoshi , Kanai Takanori , Nakamoto Nobuhiro 
Published: January 2024

Background:
Patients with severe alcohol-associated hepatitis (SAH) have a high short-term mortality rate. Unmet needs exist in patients who are refractory to corticosteroids (CS) or are ineligible for early liver transplantation.

Methods:
This was a prospective, open-label, nonrandomized pilot study conducted at a liver transplant center in Tokyo, Japan, starting in October 2015. Lille model and Model for End-stage Liver Disease (MELD) score-defined CS nonresponsive or CS-intolerant patients with SAH who fulfilled the inclusion criteria (leukocytosis over 10,000/μL, etc.) were considered for enrollment. The median duration from admission to enrollment was 23 days (IQR, 14-31 days), after standard of care. Granulocyte-monocyte/macrophage apheresis (GMA) performed with Adacolumn twice per week, up to 10 times per treatment course, was evaluated.

Results:
13 GMA treatments were conducted through December 2021. Maddrey Discriminant Function was 53.2

17.7 at admission. The overall survival rate was 90.9% at 90 and 180 days. MELD scores significantly improved, from median (IQRs) of 23 (20–25) to 15 (13–21) after GMA (p<0.0001). Estimated mortality risks using the Lille model and MELD scores significantly improved from 20.9%±16.5% to 7.4%±7.3% at 2 months and from 30.4%±21.3% to 11.6%±10.8% at 6 months, respectively (both p<0.01), and were internally validated. The cumulative rate of alcohol relapse was 35.9% per year. No severe adverse events were observed. In exploratory analysis, granulocyte colony-stimulating factor levels were significantly correlated with prognostic systems such as MELD-Sodium scores after GMA (correlation coefficient= −0.9943, p<0.0001) but not before GMA (p=0.62).

Conclusions:
Compared to published studies, GMA is associated with a lower-than-expected 90- and 180-day mortality in patients with CS-nonresponsive or CS-intolerant SAH. GMA may meet the needs as a salvage anti-inflammatory therapy for SAH. (Trial registration: UMIN000019351 and jRCTs No.032180221) (274 words).
In Vivo Confocal Microscopy Characterization of Candida parapsilosis Keratitis
Authors: Scotto R. , Forte P. , Macrì A. , Bonzano C. , Traverso C. E. 
Published: January 2024

Abstract:
The present clinical case concerns two patients with mycotic keratitis because of Candida parapsilosis in which corneal confocal microscopy presented a characteristic feature of this pathogen. Both described patients used a therapeutic contact lens and administered a therapy with steroid eye drops which are well known predisposing factors for the onset of corneal mycoses. This report can be useful for correctly identifying the pathologic condition and quickly directing the therapy.
Safety and efficacy of extended thrombophilia screening directed venous thromboembolic events (VTE) prophylaxis in live liver donors: do we really need extended thrombophilia screening routinely?
Authors: Dogar Abdul Wahab , Hussain Azhar , Ullah Kaleem , Shams-ud-din  , Ghaffar Abdul , Abbasher Hussien Mohamed Ahmed Khabab , Junaid Tahir Muhammad 
Published: January 2024

Background and aims:
The study aimed to determine the prevalence of hereditary thrombophilia, and stratify its severity among live liver donors in Pakistan. Also, the authors evaluated the safety and efficacy of thrombophilia profile testing directed venous thromboembolic events (VTE) prophylaxis while balancing bleeding risk and the need for routine thrombophilia testing before live liver donation among living donor candidates.

Materials and methods:
Protein S (PS), protein C (PC), anti-thrombin (AT) III, and anti-phospholipid antibody panel (APLA) levels were measured in 567 potential donor candidates. Donors were divided into normal, borderline and high-risk groups based on Caprini score. The safety endpoints were VTE occurrence, bleeding complications or mortality.

Results:
Among 567 donors, 21 (3.7%) were deficient in protein C, and 14 (2.5%) were deficient in anti-thrombin-III. IgM and IgG. Anti-phospholipids antibodies were positive in 2/567 (0.4%) and 2/567 (0.4%), respectively. IgM and IgG lupus anticoagulant antibodies were positive in 3/567 (0.5%) and 3/567 (0.5%), respectively. VTE events, bleeding complications and postoperative living donors liver transplantation-related complications were comparable among the three donor groups (P>0.05). One donor in the normal donor group developed pulmonary embolism, but none of the donors in either borderline or high-risk group developed VTE. The mean length of ICU and total hospital stay were comparable. No donor mortality was observed in all donor groups.

Conclusions:
Due to thrombophilia testing directed VTE prophylaxis, VTE events were comparable in normal, borderline and high-risk thrombophilia donor groups, but more evaluations are required to determine the lower safe levels for various thrombophilia parameters including PC, PS and AT-III before surgery among living donor candidates.
Impact of transesophageal echocardiography dynamic monitoring of left ventricular preload on postoperative gastrointestinal function in colorectal cancer patients undergoing radical surgery
Authors: du Jingjing , Zhang Tianyu , Hao Conghui , Xu Hai , Luan Hengfei , Cheng Zhi , Ding Mengyao 
Published: January 2024

Background:
Patients undergoing intestinal tumour surgery are fasted preoperatively for a series of bowel preparations, which makes it difficult to assess the patients’ volume, posing a challenge to intraoperative fluid replacement. Besides, inappropriate fluid therapy can cause organ damage and affect the prognosis of patients, and it increases the burden of patients and has a certain impact on patients and families.

Material and methods:
The authors designed a single-centre, prospective, single-blinded, randomized, parallel-controlled trial. Fifty-four patients undergoing elective radical resection of colorectal cancer were selected and divided into two groups according to whether transesophageal echocardiography (TEE) was used or not during the operation, that is the goal-directed fluid therapy (GDFT) group (group T) guided by TEE and the restrictive fluid therapy group (group C). Fluid replacement was guided according to left ventricular end-diastolic volume index (LVEDVI) in group T and according to restrictive fluid replacement regimen in group C.

Results:
The first postoperative exhaust time and defecation time in group T [(45±21), (53±24) h] were significantly shorter (P<0.05) than those in group C [(63±26), (77±30) h]. There were no significant differences (P>0.05) in liquid intake time and postoperative nausea and vomiting incidences between the two groups. The total intraoperative fluid volume in group T was significantly higher (P<0.05) than that in group C. There was no significant difference (P>0.05) in urine volume between the two groups. There were no significant differences (P>0.05) in lactate content, mean arterial pressure, and heart rate at various time points between the two groups. The length of hospital stay in group C [(18±4) days] was significantly longer (P<0.05) than that in group T [(15±4) days].

Conclusions:
For patients undergoing colorectal cancer surgery, fluid therapy by monitoring LVEDVI resulted in faster recovery of gastrointestinal function and shorter hospital stay.
Refractory Anti–N-Methyl-d-Aspartate Receptor Autoimmune Encephalitis Induced by Ovarian Teratoma: A Case Report
Authors: Zhang Rui , Zhao Xuemei , Li Wenjing , Gao Yu 
Published: January 2024

Objective
Teratoma is a type of germ cell tumor that derived from early embryonic stem cells and germ cell lines, which can lead to a rare complication known as paraneoplastic encephalitis syndrome. Delayed removal of teratoma allows for continuing antigen presentation, inducing affinity maturation of the antibody and the generation of long-lived plasma cells that infiltrate both bone marrow and brain, which makes the patient nonresponsive to later removal of teratoma and refractory to immunotherapy. We present this rare case to remind clinicians to be vigilant for the recognition and removal of teratoma during the treatment of autoimmune encephalitis.

Methods
We retrospectively reviewed the clinical record of this 12-year 5-month-old female patient diagnosed with anti–N-methyl-d-aspartate receptor (anti-NMDAR) autoimmune encephalitis; her ovarian teratoma was unidentified on admission. She did not respond to immunosuppressive therapy until the mature ovarian teratoma identified 45 days after admission and removed the following day, nearly 2 months after symptom onset. This patient experienced nearly complete resolution of symptoms within the subsequent 2 weeks. In addition, we conducted a literature review of the clinical presentations and treatment of anti-NMDAR autoimmune encephalitis associated with ovarian teratoma in the pediatric population.

Results
Our findings suggest that clinicians should be vigilant for the recognition and removal of teratoma during the treatment of autoimmune encephalitis.

Conclusion
Female pediatric patients with suspected anti-NMDAR encephalitis should be screened for ovarian tumors immediately and treated in a multidisciplinary setting including neurology and obstetrics and gynecology.
A large-scale cancer-specific protein-DNA interaction network
Authors: Lu Yunwei , Berenson Anna , Lane Ryan , Guelin Isabelle , Li Zhaorong , Chen Yilin , Shah Sakshi , Yin Meimei , Soto-Ugaldi Luis Fernando , Fiszbein Ana , Fuxman Bass Juan Ignacio 
Published: January 2024

AbstractCancer development and progression are generally associated with dysregulation of gene expression, often resulting from changes in transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network as well as an extensive promoter clone resource for future studies. Most highly connected TFs do not show a preference for binding to promoters of genes associated with either good or poor cancer prognosis, suggesting that emerging strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activator or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF estrogen receptor ɑ (ESR1) on DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study not only broadens our knowledge of TFs involved in the cancer gene regulatory network but also provides a valuable resource for future studies, laying a foundation for potential therapeutic strategies targeting TFs in cancer.
Optimal Phylogenetic Reconstruction of Insertion and Deletion Events
Authors: Tule Sanjana , Foley Gabriel , Zhao Chongting , Forbes Michael , Bodén Mikael 
Published: January 2024

AbstractInsertions and deletions (indels) influence the genetic code in fundamentally distinct ways from substitutions, significantly impacting gene product structure and function. Despite their influence, the evolutionary history of indels is often neglected in phylogenetic tree inference and ancestral sequence reconstruction, hindering efforts to comprehend biological diversity determinants and engineer variants for medical and industrial applications.We frame determining the optimal history of indel events as a single Mixed-Integer Programming (MIP) problem, across all nodes in a phylogenetic tree adhering to topological constraints, and all sites implied by a given set of aligned, extant sequences. By disentangling the impact on ancestral sequences at each branch point, this approach identifies the minimal indel events that jointly explain the diversity in sequences mapped to the tips of that tree. MIP can recover alternate optimal indel histories, if available.We evaluated MIP for indel inference on a dataset comprising 15 real phylogenetic trees associated with protein families ranging from 165 to 2000 extant sequences, and on 60 synthetic trees at comparable scales of data and reflecting realistic rates of mutation. Across relevant metrics, MIP outperformed alternative parsimony-based approaches and reported the fewest indel events, on par or below their occurrence in synthetic datasets. MIP offers a rational justification for indel patterns in extant sequences; importantly, it uniquely identifies global optima on complex protein data sets without making unrealistic assumptions of independence or evolutionary underpinnings, promising a deeper understanding of molecular evolution and aiding novel protein design.
Optimizing Accuracy and Efficiency in Analyzing Non-UMI Liquid Biopsy Datasets Using the Sentieon ctDNA Pipeline
Authors: Niu Li , Hu Jinnan , Chen Chuan , Jiang Cai , Chen Haodong , Tang Gongcheng , Liu Ying , Liu Yi 
Published: January 2024

AbstractSequencing clinical liquid biopsy, especially circulating tumor DNA (ctDNA), provides a valuable method for identifying low allele frequency tumor variants, opening novel clinical applications, particularly in treatment selection for late-stage cancer patients. Despite advancements, challenges in assay development persist, primarily due to limited sample volumes and insufficiency of reads supporting low allele frequency variants. The allele frequencies of clinically significant variants often hover close to the threshold of errors introduced by PCR and sequencing processes. Therefore, more sophisticated analysis methods are crucial to further reduce base error rates, enabling accurate discrimination between background errors and genuine somatic variants. While several ctDNA analysis pipelines have been published and adopted, there is room for improvement in terms of accuracy and run efficiency.In this study, we introduce Sentieon’s innovative consensus-based ctDNA pipeline - a rapid and precise solution for calling small somatic variants from non-UMI ctDNA sequencing data. The pipeline comprises four core modules: alignment, consensus generation, variant calling, and variant filtering. Through benchmarking with in-vitro and real clinical datasets, we observed that the Sentieon ctDNA pipeline exhibits higher accuracy compared to alternative methods.
Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA
Authors: Martínez-García Lourdes , Pulido Angélica , Ferrari Giada , Hufthammer Anne Karin , Vedeler Marianne , Hirons Alex , Kneale Catherine , Barrett James H. , Star Bastiaan 
Published: January 2024

AbstractMarine resources have been important for the survival and economic development of coastal human communities across northern Europe for centuries. Knowledge of the origin of such historic resources can provide key insights into fishing practices and the spatial extent of trade networks. Here, we combine ancient DNA and stable isotopes (δ13C, δ15N, non-exchangeable δ2H and δ34S) to investigate the geographical origin of archaeological cod remains in Oslo from the eleventh to seventeenth centuries CE. Our findings provide genetic evidence that Atlantic cod was obtained from different sources, including a variety of distant-water populations like northern Norway and possibly Iceland. Evidence for such long-distance cod trade is already observed from the eleventh century, contrasting with archaeological and historical evidence from Britain and other areas of Continental Europe around the North and Baltic Seas, where such trade developed in a later period. Diverse biological origins are further supported by significant differences of a range of isotopes, indicating that multiple populations living in different environments were exploited. This research highlights the utility of combining ancient DNA methods and stable isotope analysis to describe the development of marine fisheries during the medieval and post-medieval period.
A Biophysical Model for ATAC-seq Data Analysis
Authors: Felce Catherine , Gorin Gennady , Pachter Lior 
Published: January 2024

ABSTRACTThe Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) can be used to identify open chromatin regions, providing complementary information to RNA-seq which measures gene expression by sequencing. Single-cell “multiome” methods offer the possibility of measuring both modalities simultaneously in cells, raising the question of how to analyze them jointly, and also the extent to which the information they provide is better than unregistered data where single-cell ATAC-seq and single-cell RNA-seq are performed on the same sample, but on different cells. We propose and motivate a biophysical model for chromatin dynamics and subsequent transcription that can be used with multiome data, and use it to assess the benefits of multiome data over unregistered single-cell RNA-seq and single-cell ATAC-seq. We also show that our model provides a biophysically grounded approach to integration of open chromatin data with other modalities.
Application of hybrid failure mode effect analysis based on fuzzy AHP and fuzzy TOPSIS in quality risk assessment of fixed-dose artemether-lumefantrine tablets
Authors: Ilyasu Salim , Malami Sani , Khalid Garba Mohammed , Abdussalam Umar Sharif , Dawud Abubakar Magaji , Mohammed Saratu , Falalu Al-Kasim Rabiu , Zaharadeen Mustapha Fatima , Sani Farouq Idris , Manu Abdussalam Yayo , Yakasai Ibrahim Adamu , Chedi Basheer Abba-Zubair , Bello Aminu Sahalu , Ibrahim Adam Bashir , Julde Saadatu , Idris Maryam Shehu , Bichi Lawal Alhassan 
Published: January 2024

AbstractBackgroundA hybrid Failure Mode Effect Analysis (FMEA) based on fuzzy logic and multicriteria decision analytics was applied as a post-marketing surveillance tool for troubleshooting potential quality problems of Artemisinin Combination Therapies (ACTs) as a means of aggregating subjective opinions of quality experts in providing vital information for continuous management and improvement of safety and quality standards.Research design and methodsAn FMEA team of five cross-functional quality experts implemented a hybrid fuzzy FMEA model based on Analytical Hierarchy Process (AHP) and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) to solve multicriteria decision problems in quality risk analysis of historic quality control data of ACTs.ResultsExpert opinions were captured as triangular fuzzy numbers to represent the linguistic scoring of risk-determining variables for fifteen failure modes. The fuzzy AHP enabled systematic ranking of the variables, while the fuzzy TOPSIS algorithm provided easily understood and configurable computational procedures for ranking the failure modes based on optimal geometric paths to positive and negative ideal solutions.ConclusionsThe quality risk of ACTs could be reliably established using the fuzzy FMEA where aggregated experts’ decisions and risk variables’ weights are of considerable importance to the final ranking of quality failures.