bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of reference genes for transcript analyses in Komagataella phaffii (Pichia pastoris)
Authors: Besleaga Mihail , Vignolle Gabriel A. , Kopp Julian , Spadiut Oliver , Mach Robert L. , Mach-Aigner Astrid R. , Zimmermann Christian 
Published: March 2023

Abstract
Background
The yeast Komagataella phaffii (Pichia pastoris) is routinely used for heterologous protein expression and is suggested as a model organism for yeast. Despite its importance and application potential, no reference gene for transcript analysis via RT-qPCR assays has been evaluated to date. In this study, we searched publicly available RNASeq data for stably expressed genes to find potential reference genes for relative transcript analysis by RT-qPCR in K. phaffii. To evaluate the applicability of these genes, we used a diverse set of samples from three different strains and a broad range of cultivation conditions. The transcript levels of 9 genes were measured and compared using commonly applied bioinformatic tools.

Results
We could demonstrate that the often-used reference gene ACT1 is not very stably expressed and could identify two genes with outstandingly low transcript level fluctuations. Consequently, we suggest the two genes, RSC1, and TAF10 to be simultaneously used as reference genes in transcript analyses by RT-qPCR in K. phaffii in future RT-qPCR assays.

Conclusion
The usage of ACT1 as a reference gene in RT-qPCR analysis might lead to distorted results due to the instability of its transcript levels. In this study, we evaluated the transcript levels of several genes and found RSC1 and TAF10 to be extremely stable. Using these genes holds the promise for reliable RT-qPCR results.
A dual functional Ti-Ga alloy: inhibiting biofilm formation and osteoclastogenesis differentiation via disturbing iron metabolism
Authors: Li Fupeng , Huang Kai , Wang Jinbing , Yuan Kai , Yang Yiqi , Liu Yihao , Zhou Xianhao , Kong Keyu , Yang Tao , He Jian , Liu Chunjie , Ao Haiyong , Liu Fengxiang , Liu Qian , Tang Tingting , Yang Shengbing 
Published: March 2023

Abstract

Background
Although biomedical implants have been widely used in orthopedic treatments, two major clinical challenges remain to be solved, one is the bacterial infection resulting in biofilm formation, and the other is aseptic loosening during implantation due to over-activated osteoclastogenesis. These factors can cause many clinical issues and even lead to implant failure. Thus, it is necessary to endow implants with antibiofilm and aseptic loosening-prevention properties, to facilitate the integration between implants and bone tissues for successful implantation. To achieve this goal, this study aimed to develop a biocompatible titanium alloy with antibiofilm and anti-aseptic loosening dual function by utilizing gallium (Ga) as a component.

Methods

A series of Ti-Ga alloys were prepared. We examined the Ga content, Ga distribution, hardness, tensile strength, biocompatibility, and anti-biofilm performance in vitro and in vivo. We also explored how Ga
3+
ions inhibited the biofilm formation of
Staphylococcus aureus
(
S. aureus
) and
Escherichia coli
(
E. coli
) and osteoclast differentiation.

Results

The alloy exhibited outstanding antibiofilm properties against both
S. aureus
and
E. coli
in vitro and decent antibiofilm performance against
S. aureus
in vivo. The proteomics results demonstrated that Ga
3+
ions could disturb the bacterial Fe metabolism of both
S. aureus
and
E. coli
, inhibiting bacterial biofilm formation. In addition, Ti-Ga alloys could inhibit receptor activator of nuclear factor-κB ligand (RANKL)-dependent osteoclast differentiation and function by targeting iron metabolism, then suppressing the activation of the NF-κB signaling pathway, thus, showing their potential to prevent aseptic loosening.

Conclusion

This study provides an advanced Ti-Ga alloy that can be used as a promising orthopedic implant raw material for various clinical scenarios. This work also revealed that iron metabolism is the common target of Ga
3+
ions to inhibit biofilm formation and osteoclast differentiation.
Visual function and retinal morphological changes after single suprachoroidal delivery of fluocinolone acetonide (Iluvien®) implant in eyes with chronic diabetic macular edema
Authors: El Rayes Ehab N. , Leila Mahmoud 
Published: March 2023

Abstract
Background
To assess the efficacy and safety of supra-choroidal (SC) Iluvien in the management of chronic diabetic macular edema (DME).

Methods
A retrospective interventional non-comparative consecutive case series including patients with chronic DME who received an SC Iluvien implant. All patients had persistent central macular thickness (CMT) ≥ 300µ after previous treatment with anti-vascular endothelial growth factor (VEGF) agents or laser photocoagulation. The main outcome measures were improvement of best-corrected visual acuity (BCVA), reduction of CMT, and detection of ocular hypertension/glaucoma or cataract formation. Friedman’s two-way ANOVA was used to analyze BCVA, intraocular pressure (IOP), and DME across different time points. P-value = 0.05.

Results
The study included 12 eyes of 12 patients. Six patients (50%) were males. The median age was 58 years (range 52–76 years). The median duration of DM was 13 years (range 8–20 years). Ten patients (83.3%) were phakic and 2 patients (17%) were pseudophakic. The median pre-operative BCVA was 0.07 (range 0.05–0.8). The median pre-operative CMT was 544µ (range 354–745µ). The median pre-operative IOP was 17 mmHg (range 14-21mmHg). The median follow-up period was 12 months, range (12–42). Post-operatively, the median final BCVA was 0.15 (range 0.03-1), p 0.02, the median CMT was 404µ (range 213–747), p 0.4 and the median IOP was 19.5 mmHg (range 15–22), p 1. Two out of 10 phakic patients (20%) developed nuclear sclerosis grade I by 12 months. Six patients (50%) developed a transient rise in IOP < 10 mmHg from the baseline that resolved within 3 weeks with antiglaucoma drops.

Conclusion
SC Iluvien is potentially effective in improving visual function, reducing macular edema, and reducing the incidence of steroid-induced cataracts and glaucoma.
The role of working memory capacity in soccer tactical decision making at different levels of expertise
Authors: Glavaš Dragan , Pandžić Mario , Domijan Dražen 
Published: March 2023

AbstractAthletic skills acquired through deliberate practice are essential for expert sports performance. Some authors even suggest that practice circumvents the limits of working memory capacity (WMC) in skill acquisition. However, this circumvention hypothesis has been challenged recently by the evidence that WMC plays an important role in expert performance in complex domains such as arts and sports. Here, we have used two dynamic soccer tactical tasks to explore the effect of WMC on tactical performance at different levels of expertise. As expected, professional soccer players exhibited better tactical performance than amateur and recreational players. Furthermore, WMC predicted faster and more accurate tactical decisions in the task under auditory distraction and faster tactical decisions in the task without distraction. Importantly, lack of expertise × WMC interaction suggests that the WMC effect exists at all levels of expertise. Our results speak against the circumvention hypothesis and support a model of independent contributions of WMC and deliberate practice on expert performance in sports.
Association between the single-nucleotide polymorphism (rs1030868) variant in matrix metallopeptidase 2 gene and the development of lymphedema
Authors: Shakra Mohammed Youssef , Ibrahim Sherief , El Shahat Mostafa , Mohamed Amr , Sharapy Alaa , Omar Adel , AlSaeed Alshaimaa 
Published: March 2023

AbstractBackgroundUnderstanding the genetic and molecular pathophysiology of lymphedema contributes to the identification of the complex interaction of genes associated with lymphedema and provides a key therapeutic opportunity to restore lymphatic function. This study aims to answer whether the single-nucleotide polymorphism (SNP) rs1030868 in the MMP-2 gene could be an associated variant in lymphedema development.MethodsThis study was carried out on 93 lymphedema cases (patients’ group) and 187 healthy individuals (control group). Genotyping of MMP-2 (rs1030868) was done following the protocol of Custom TaqMan® SNP Genotyping Assays. TaqMan™ Fast Advanced Master Mix (Cat# 4448892) was used.ResultsThe risk alleles for MMP-2 SNP rs1030868 were A and G of lymphedema development. The GG genotype was associated with triple the risk of lymphedema (OR 3.2, 95% CI 1.2–6.5,p = 0.019), while the AA genotype was associated with 5.9 times the likelihood of lymphedema (OR 5.9, 95% CI 2.3–11.9,p < 0.001).ConclusionsWe concluded that the single-nucleotide polymorphisms of rs1030868 in the matrix metallopeptidase 2 gene (allele A and allele G) could be associated variants with the development of lymphedema.
A surgical case of ciliated muconodular papillary tumor of the lung
Authors: Shidei Hiroaki , Aoshima Hiroe , Ogihara Akira , Isaka Tamami , Onizuka Hiromi , Nagashima Yoji , Nakatani Yukio , Kanzaki Masato 
Published: March 2023

AbstractCiliated muconodular papillary tumor (CMPT) is a rare type of tumor with both benign and malignant characteristics. Herein, we report the surgical case of a 65-year-old man with CMPT. Chest computed tomography revealed a solitary cavitary lesion with a maximum diameter of 11-mm in S10b of the right lower lung. A thoracoscopic lung wedge resection was subsequently performed. On microscopic examination, the tumor was composed of highly columnar cells with tubular-to-papillary and cystic growth patterns. On immunostaining, it was positive for the epidermal growth factor receptor. The tumor was diagnosed as a CMPT, exhibiting no recurrence after two years of follow-up.
Successful management of recurrence of lung surgery-induced pyoderma gangrenosum after pacemaker implantation: a case report
Authors: Muto Jun , Hase Ryunosuke , Narita Sho , Otsuka Shouhei , Sasaki Akihiro , Kato Tatsuya 
Published: March 2023

Abstract
Background
Pyoderma gangrenosum begins as a painful erythema with induration, vesicles, or hemorrhagic pustules, which develops into serous ulcers. In addition to ulcerative colitis and myelodysplastic syndrome, surgical intervention may also induce this disease.

Case presentation
A 90-year-old man had previously undergone video-assisted thoracic surgery left upper lobectomy for left lung cancer. Blood tests on the 6th postoperative day showed elevated levels of white blood cells and C-reactive protein. The wound appeared red and drained pus; however, the wound culture was negative for bacteria. A skin biopsy was performed on the 13th postoperative day, and the patient was diagnosed with pyoderma gangrenosum. Tacrolimus hydrate ointment was administered, symptoms gradually improved around the 18th postoperative day, and the erythematous area shrank. The patient was discharged on the 50th postoperative day.
Six months after lung surgery, a pacemaker was implanted in the left subclavian region. On the 6th postoperative day, the wound appeared reddish-brown and exudate was observed. On the 10th postoperative day, wound dehiscence was observed, and the pacemaker was removed. The patient was diagnosed with recurrent pyoderma gangrenosum and was re-treated with ointment. On the 29th postoperative day, a leadless pacemaker, which can be implanted with a small incision, was selected for treating arrhythmia. The patient was discharged 7 days after the second implantation.

Conclusion
We report a recurrent pyoderma gangrenosum case following lung cancer surgery after pacemaker implantation as the second surgery, in which disease recurrence could be prevented by changing to a leadless pacemaker. Surgery and other invasive procedures should be avoided in pyoderma gangrenosum patients.
Smoking Cessation After Diagnosis of Kidney Cancer Is Associated With Reduced Risk of Mortality and Cancer Progression: A Prospective Cohort Study
Authors: Sheikh Mahdi , Mukeriya Anush , Zahed Hana , Feng Xiaoshuang , Robbins Hilary A. , Shangina Oxana , Matveev Vsevolod , Brennan Paul , Zaridze David 
Published: March 2023

PURPOSE To investigate whether postdiagnosis smoking cessation may affect the risk of death and disease progression in patients with renal cell carcinoma (RCC) who smoked at the time of diagnosis. METHODS Two hundred twelve patients with primary RCC were recruited between 2007 and 2016 from the Urological Department in N.N. Blokhin National Medical Research Center of Oncology, Moscow, Russia. Upon enrollment, a structured questionnaire was completed, and the patients were followed annually through 2020 to repeatedly assess their smoking status and disease progression. Survival probabilities and hazards for all-cause and cancer-specific mortality and disease progression were investigated using extended the Kaplan-Meier method, time-dependent Cox proportional hazards regression, and Fine-Gray competing-risk models. RESULTS Patients were followed for a median of 8.2 years. During this time, 110 cases of disease progression, 100 total deaths, and 77 cancer-specific deaths were recorded. Eighty-four patients (40%) quit smoking after diagnosis. The total person-years at risk for this analysis were 748.2 for continuing smoking and 611.2 for quitting smoking periods. At 5 years of follow-up, both overall survival (85% v 61%) and progression-free survival (80% v 57%) rates were higher during the quitting than continuing smoking periods (both P < .001). In the multivariable time-dependent models, quitting smoking was associated with lower risk of all-cause mortality (hazard ratio [HR], 0.51; 95% CI, 0.31 to 0.85), disease progression (HR, 0.45; 95% CI, 0.29 to 0.71), and cancer-specific mortality (HR, 0.54; 95% CI, 0.31 to 0.93). The beneficial effect of quitting smoking was evident across all subgroups, including light smokers versus moderate-heavy smokers and those with early-stage versus late-stage tumors. CONCLUSION Quitting smoking after RCC diagnosis may significantly improve survival and reduce the risk of disease progression and cancer mortality among patients who smoke.
Response to Neoadjuvant Therapy and Long-Term Survival in Patients With Triple-Negative Breast Cancer
Authors: Liedtke Cornelia , Mazouni Chafika , Hess Kenneth R. , André Fabrice , Tordai Attila , Mejia Jaime A. , Symmans W. Fraser , Gonzalez-Angulo Ana M. , Hennessy Bryan , Green Marjorie , Cristofanilli Massimo , Hortobagyi Gabriel N. , Pusztai Lajos 
Published: March 2023

PURPOSE Triple-negative breast cancer (TNBC) is defined by the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2) expression. In this study, we compared response to neoadjuvant chemotherapy and survival between patients with TNBC and non-TNBC. PATIENTS AND METHODS Analysis of a prospectively collected clinical database was performed. We included 1,118 patients who received neoadjuvant chemotherapy at M.D. Anderson Cancer Center for stage I-III breast cancer from 1985 to 2004 and for whom complete receptor information were available. Clinical and pathologic parameters, pathologic complete response rates (pCR), survival measurements, and organ-specific relapse rates were compared between patients with TNBC and non-TNBC. RESULTS Two hundred fifty-five patients (23%) had TNBC. Patients with TNBC compared with non-TNBC had significantly higher pCR rates (22% v 11%; P = .034), but decreased 3-year progression-free survival rates ( P < .0001) and 3-year overall survival (OS) rates ( P < .0001). TNBC was associated with increased risk for visceral metastases ( P = .0005), lower risk for bone recurrence ( P = .027), and shorter postrecurrence survival ( P < .0001). Recurrence and death rates were higher for TNBC only in the first 3 years. If pCR was achieved, patients with TNBC and non-TNBC had similar survival ( P = .24). In contrast, patients with residual disease (RD) had worse OS if they had TNBC compared with non-TNBC ( P < .0001). CONCLUSION Patients with TNBC have increased pCR rates compared with non-TNBC, and those with pCR have excellent survival. However, patients with RD after neoadjuvant chemotherapy have significantly worse survival if they have TNBC compared with non-TNBC, particularly in the first 3 years.
Data reconstruction for complex flows using AI: Recent progress, obstacles, and perspectives
Authors: Buzzicotti Michele 
Published: March 2023

Abstract
In recent years the fluid mechanics community has been intensely focused on pursuing solutions to its long-standing open problems by exploiting the new machine learning (ML) approaches. The exchange between ML and fluid mechanics is bringing important paybacks in both directions. The first is benefiting from new physics-inspired ML methods and a scientific playground to perform quantitative benchmarks, whilst the latter has been open to a large set of new tools inherently well suited to deal with big data, flexible in scope, and capable of revealing unknown correlations. A special case is the problem of modeling missing information of partially observable systems. The aim of this paper is to review some of the ML algorithms that are playing an important role in the current developments in this field, to uncover potential avenues, and to discuss the open challenges for applications to fluid mechanics.
Significance of classically forbidden regions for short baseline neutrino experiments
Authors: Ahluwalia Dharam Vir 
Published: March 2023

Abstract
Classically forbidden regions (CFRs) are common to both non-relativistic quantum mechanics, and to relativistic quantum field theory. It is known since 2001 that CFR contributes roughly sixteen percent of energy to the ground state of a simple harmonic oscillator (Adunas G. Z. et al., Gen. Relativ. Gravit., 33 (2001) 183). Similarly, quantum field theoretic arguments yield a non-zero amplitude for a massive particle to cross the light cone (that is, into the CFR). The signs of these amplitudes are opposite for fermions and antifermions. This has given rise to an erroneous conclusion that amplitude to cross the light cone is identically zero. This is true as long as a measurement does not reveal the considered object to be a particle or antiparticle. However, neutrino oscillation experiments do measure a neutrino ν, or an antineutrino

. Here we show that in the context of neutrino oscillations these observations have the potential to resolve various short baseline anomalies for a sufficiently light lowest mass eigenstate. In addition, we make a concrete prediction for the upcoming results to be announced later this year by JSNS2.
Size of a 2D ring polymer topologically unentangled with a planar array of obstacles
Authors: Daniels D. R. 
Published: March 2023

Abstract
We readdress the statistical mechanical problem of the size of a 2D ring polymer, topologically unentangled with a planar lattice array of regularly spaced obstacles. It is commonly assumed in the literature that such a polymer adopts a randomly branched type of configuration, in order to ostensibly maximise chain entropy, while minimising obstacle entanglement. Via an innovative analytic approach, valid in the condensed polymer region, we are able to provide a greater theoretical understanding, and justification, for this presumed polymer behaviour. Our theoretically derived results could also potentially have important implications for the structure of interphase chromosomes, as well as electrophoretic ring polymer dynamics.
Oncological Outcome After Lymph Node Dissection for Cutaneous Squamous Cell Carcinoma
Authors: Huis in ’t Veld Eva A. , Boere Thomas , Zuur Charlotte L. , Wouters Michel W. , van Akkooi Alexander C. J. , Haanen John B. A. G. , Crijns Marianne B. , Smith Myles J. , Mooyaart Antien , Wakkee Marlies , Sewnaik Aniel , Strauss Dirk C. , Grunhagen Dirk J. , Verhoef Cornelis , Hayes Andrew J. , van Houdt Winan J. 
Published: March 2023

Abstract
Background
Although cutaneous squamous cell carcinoma (cSCC) is common, lymph node metastases are relatively rare and are usually treated with lymph node dissection (LND). The aim of this study was to describe the clinical course and prognosis after LND for cSCC at all anatomical locations.

Methods
A retrospective search at three centres was performed to identify patients with lymph node metastases of cSCC who were treated with LND. Prognostic factors were identified by uni- and multivariable analysis.

Results
A total of 268 patients were identified with a median age of 74. All lymph node metastases were treated with LND, and 65% of the patients received adjuvant radiotherapy. After LND, 35% developed recurrent disease both locoregionally and distantly. Patients with more than one positive lymph node had an increased risk for recurrent disease.
165 (62%) patients died during follow-up of whom 77 (29%) due to cSCC. The 5-year OS- and DSS rate were 36% and 52%, respectively. Disease-specific survival was significantly worse in immunosuppressed patients, patients with primary tumors >2cm and patients with more than one positive lymph node.

Conclusions
This study shows that LND for patients with lymph node metastases of cSCC leads to a 5-year DSS of 52%. After LND, approximately one-third of the patients develop recurrent disease (locoregional and/or distant), which underscores the need for better systemic treatment options for locally advanced cSCC. The size of the primary tumor, more than one positive lymph node, and immunosuppression are independent predictors for risk of recurrence and disease-specific survival after LND for cSCC.
Revisiting dynamic range and image enhancement ability of contemporary digital radiographic systems—part 2: a subjective assessment
Authors: Marinho-Vieira Luiz Eduardo , Martins Luciano Augusto Cano , Freitas Deborah Queiroz , Haiter-Neto Francisco , Oliveira Matheus L. 
Published: March 2023

Objective: To assess the subjective image quality of original and manually enhanced radiographs acquired at different X-ray exposure times and using different digital systems. Methods: A total of 500 radiographs obtained under 10 exposure times, 5 digital systems, and 2 enhancement conditions were assessed by 5 observers, who were asked to categorize each radiograph into acceptable or unacceptable. A radiograph was considered to be acceptable when at least four out of five observers found it acceptable. Descriptive analysis was used to summarize the outcomes and compare the subjective image quality of original and manually enhanced digital radiographs among different X-ray exposure times and digital systems. Results: Express had six exposure times producing acceptable original images within a range from 0.063 to 0.4 s, followed by Digora Toto, which had five within a range from 0.063 to 0.32 s, Digora Optime, which had four within a range from 0.063 to 0.2 s,and SnapShot and VistaScan, which had 2 (0.2 and 0.32 s) and 1 (0.63 s), respectively. Image enhancement turned unacceptable images into acceptable ones in four digital systems: SnapShot at three exposure times, Digora Toto at two exposure times, Express at one exposure time, and VistaScan at four exposure times. Conclusion: Image enhancement based on brightness and/or contrast adjustments may be necessary to reveal the useful dynamic range of some digital radiographic systems and PSP-based systems may not necessarily have a wider range than sensor-based systems.