bluuebunny/crossref_metadata_2025_split huggingface dataset:
The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure
Authors: Hertel Sophie , Spinney Richard E , Xu Stephanie Y , Ouldridge Thomas E , Morris Richard G , Lee Lawrence K 
Published: July 2022

Abstract
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson–Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.
Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment
Authors: Bai Tanxi , Zhang Jiayi , Huang Kai , Wang Wen , Chen Bowen , Li Yujie , Zhao Mengyao , Zhang Suoyu , Zhu Chenyou , Liu Dongsheng , Wei Bryan 
Published: July 2022

AbstractEnzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration. A careful calibration of ligation efficiency is performed on structures with programmable nicks. Systematic investigation using comparative agarose gel electrophoresis enables quantitative assessment of enhanced survivability with ligation treatment on a number of unique structures. The solid ligation performance sets up the foundation for the ligation-based structural reconfiguration. With the capability of switching base pairing status between permanent and transient (ON and OFF) by a simple round of enzymatic treatment, ligation induced reconfiguration can be engineered for DNA nanostructures accordingly.
The kidney reabsorption-related magnesium depletion score is associated with increased likelihood of abdominal aortic calcification among US adults
Authors: Lu Jian , Li Han , Wang Shixiang 
Published: July 2022

ABSTRACT

Background
Kidney reabsorption plays a vital role in magnesium homeostasis. This study aimed to determine the relationship between the kidney reabsorption-related magnesium depletion score (MDS) and abdominal aortic calcification (AAC).

Methods
We obtained data for 2640 individuals from the National Health and Nutrition Examination Survey database and analysed the relationship between the MDS and AAC score. The MDS is a scoring system developed to predict the status of magnesium deficiency that fully considers the pathophysiological factors influencing the kidneys’ reabsorption capability. AAC was quantified by the Kauppila score system based on dual-energy X-ray absorptiometry. We performed stratified analysis and multiple equation regression analysis. R and EmpowerStats were used for data analysis.

Results
A total of 2640 participants were included with the mean AAC score of 1.47 ± 0.07. Participants with higher MDSs tended to have higher AAC scores [MDS 0: 0.75 (0.56–0.93), MDS 1: 1.02 (0.84–1.21), MDS 2: 2.34 (1.80–2.87), MDS 3: 3.19 (2.46–3.92), MDS ≥4: 4.99 (3.49–6.49)]. Compared with those with an MDS of 0, the highest subgroup (MDS ≥4) was associated with a higher AAC score {β = 4.24 [95% confidence interval (CI) 2.78–5.70], P &lt; .001} and the association was not altered [β = 1.81 (95% CI 0.54–3.09), P = .002] after adjusting for numerous covariates. Subgroup analyses showed that stronger associations between the MDS and AAC score were detected in adults with lower levels of magnesium intake and older age (all P for interaction &lt;.05).

Conclusions
The MDS is a promising tool for identifying individuals with magnesium deficiency status who may benefit from dietary magnesium supplementation to reduce the risks of AAC.
Utility of contrast-enhanced magnetic resonance lymphangiography for yellow nail syndrome with lymphangiopathy: a case report
Authors: Shimanuki Yui , Miyoshi Shion , Anzai Nanami , Usui Yusuke , Shiraga Nobuyuki , Kishi Kazuma 
Published: July 2022

ABSTRACT
Yellow nail syndrome (YNS) is a rare disorder characterized by the triad of yellow nails, lymphedema and chronic respiratory manifestations. Lymphatic abnormalities are a characteristic finding of YNS. Nevertheless, proof of lymphatic vessel abnormality by direct needle puncture for contrast agent injection is technically challenging because the lymphatic vessels in YNS are dysplastic. Thus, we opted for contrast-enhanced magnetic resonance (MR) lymphangiography with subcutaneous injection in patients suspected of YNS to facilitate easier comprehensive lymphatic vessel visualization. The lymphatic vessels of the thighs were few and barely recognizable, indicating weak flow cranially and lymphatic vessel hypoplasia. These findings were suggestive of dysplasia of the lymphatic vessels. Therefore, MR lymphangiography may be a useful novel diagnostic modality for YNS.
Unmasking latent extrapulmonary tuberculosis with newly diagnosed HIV-1 infection in a COVID-19 patient with prolonged fever
Authors: Hirata Kaiho , Watanabe Koji , Sasaki Takeshi , Yoshimasu Takashi , Shimomura Akihiko , Ando Naokatsu , Yanagawa Yasuaki , Mizushima Daisuke , Teruya Katsuji , Kikuchi Yoshimi , Oka Shinichi , Tsukada Kunihisa 
Published: July 2022

ABSTRACT
Prolonged fever is a common symptom of COVID-19 infection. However, other febrile diseases continue during the pandemic. Herein, we report a COVID-19-infected patient with prolonged fever despite the lack of oxygen requirement, who was finally diagnosed with tuberculotic lymphadenitis and HIV-1 infection. All symptoms improved rapidly after the initiation of antituberculosis medications. Tuberculosis is an important differential diagnosis for patients with prolonged fever during the COVID-19 pandemic. It is possible that COVID-19 infection could serve to unmask latent infections via a cytokine storm.
Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time
Authors: Corcoran Emma Tung , LeBlanc Chantal , Huang Yi-Chun , Arias Tsang Mia , Sarkiss Anthony , Hu Yuzhao , Pedmale Ullas V , Jacob Yannick 
Published: July 2022

Abstract
Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system is currently available in plants for the direct assessment of histone function. In this work, we present the development of a genetic strategy in Arabidopsis (Arabidopsis thaliana) whereby modified histone H4 transgenes can completely replace the expression of endogenous histone H4 genes. Accordingly, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate its utility, we screened this new H4 mutant collection to uncover substitutions in H4 that alter flowering time. We identified different mutations in the H4 tail (H4R17A) and the H4 globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) that strongly accelerate the floral transition. Furthermore, we identified a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants: As with other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in Arabidopsis and a roadmap to replicate this strategy for studying other histone proteins in plants.
It Takes Two to Borrow: The Effects of the Equal Credit Opportunity Act on Housing, Credit, and Labor Market Decisions of Married Couples
Authors: Bartscher Alina Kristin 
Published: July 2022

Abstract
Until the 1970s, U.S. mortgage lenders commonly discounted half of the wife’s income in couples’ joint mortgage applications. This changed with the introduction of antidiscrimination legislation in the 1970s, providing a natural experiment to study the relaxation of income-related borrowing constraints. I study the effects of the reform by estimating difference-in-differences regressions and solving a simple calibrated life cycle model. I find substantial positive effects of the reform on mortgage borrowing and homeownership rates of married couples with working wives. Moreover, I find a positive effect on married women’s labor force participation, which strongly amplifies the homeownership and borrowing effects.
Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online
The Nucleotide Revolution: Immunity at the Intersection of Toll/Interleukin-1 Receptor Domains, Nucleotides, and Ca2+
Authors: Eastman Samuel , Bayless Adam , Guo Ming 
Published: July 2022

The discovery of the enzymatic activity of the toll/interleukin-1 receptor (TIR) domain protein SARM1 five years ago preceded a flood of discoveries regarding the nucleotide substrates and products of TIR domains in plants, animals, bacteria, and archaea. These discoveries into the activity of TIR domains coincide with major advances in understanding the structure and mechanisms of NOD-like receptors and the mutual dependence of pattern recognition receptor– and effector-triggered immunity (PTI and ETI, respectively) in plants. It is quickly becoming clear that TIR domains and TIR-produced nucleotides are ancestral signaling molecules that modulate immunity and that their activity is closely associated with Ca2+signaling. TIR domain research now bridges the separate disciplines of molecular plant- and animal-microbe interactions, neurology, and prokaryotic immunity. A cohesive framework for understanding the role of enzymatic TIR domains in diverse organisms will help unite the research of these disparate fields. Here, we review known products of TIR domains in plants, animals, bacteria, and archaea and use context gained from animal and prokaryotic TIR domain systems to present a model for TIR domains, nucleotides, and Ca2+at the intersection of PTI and ETI in plant immunity.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Insights into the Catalytic Mechanism and Transition State Stabilization of 5′‐Methylthioadenosine Nucleosidase using Neutron Crystallography
Authors: Banco Michael T. , Mishra Vidhi , Ostermann Andreas , Schrader Tobias E. , Evans Gary B. , Kovalevsky Andrey Y. , Ronning Donald R. 
Published: July 2022

5′‐Methylthioadenosine nucleosidase (MTAN) is an obligatory homodimeric protein that catalyzes the hydrolysis of the N‐ribosidic bond of a variety of adenosine‐containing metabolites. The proposed catalytic mechanism of MTAN is initiated by D198 protonating the N7 position of the adenyl moiety, which consequently causes elongation and ultimate breaking of the N‐ribosidic bond, resulting in the formation of an oxocarbenium ion intermediate. Of particular interest is the pKa elevation of D198 that was proposed to have a value of 8.2, which is significantly higher than the theoretical pKa for an aspartic acid side chain. In this study we present the first joint X‐ray/neutron crystal structures of Helicobacter pylori MTAN (HpMTAN) in complex with a substrate (S‐adenosylhomocysteine), early (Formycin A) and late (p‐ClPh‐Thio‐DADMe‐ImmA) dissociative transition state analogues, as well as with the catalytic products (adenine and S‐ribosylhomocysteine). The solved X‐ray/neutron crystal structures provide the positions of exchangeable hydrogen atoms and protonation states of ionizable groups that further our understanding of the catalytic mechanism as well as the stabilization of the transition state for HpMTAN. These results confirm that the catalytic reaction is initiated by D198 functioning as a general acid through the observation of a shared deuterium atom with unconventional hydrogen bond geometry between the carboxylate group of D198 and the N7 position of adenine. Additionally, the transition state analogues neutron structures illustrate the minor differences in the hydrogen bond interactions resulting in the DADMe‐ImmA analogues being extremely potent inhibitors with Kd values in the picomolar range, despite HpMTAN shown to contain an early dissociative transition state structure.Support or Funding InformationThis work was supported by the Center for the Advancement of Science in Space via a cooperative agreement with National Aeronautics and Space Administration Grant N‐123528‐01 (to D.R.R) and by National Institute of Allergy and Infectious Disease/NIH Grant AI105084 (to D.R.R.).
Prophylactic Postoperative Noninvasive Ventilation in Adults Undergoing Upper Abdominal Surgery: A Systematic Review and Meta-Analysis
Authors: Lockstone Jane , Denehy Linda , Truong Dominic , Whish-Wilson Georgina A. , Boden Ianthe , Abo Shaza , Parry Selina M. 
Published: July 2022

OBJECTIVES:
Postoperative pulmonary complications (PPCs) are a leading cause of morbidity and mortality following upper abdominal surgery. Applying either noninvasive ventilation (NIV) or continuous positive airway pressure (CPAP) in the early postoperative period is suggested to prevent PPC. We aimed to assess whether postoperative NIV or CPAP or both prevent PPCs compared with standard care in adults undergoing upper abdominal surgery, including in those identified at higher PPC risk. Additionally, the different interventions used were evaluated to assess whether there is a superior approach.

DATA SOURCES:
We searched PubMed, Embase‚ CINAHL, CENTRAL, and Scopus from inception to May 17, 2021.

STUDY SELECTION:
We performed a systematic search of the literature for randomized controlled trials evaluating prophylactic NIV and/or CPAP in the postoperative period.

DATA EXTRACTION:
Two authors independently performed study selection and data extraction. Individual study risk of bias was assessed using the PEDro scale, and certainty in outcomes was assessed using the Grading of Recommendations Assessment, Development, and Evaluation framework.

DATA SYNTHESIS:
We included 17 studies enrolling 6,108 patients. No significant benefit was demonstrated for postoperative NIV/CPAP to reduce PPC (risk ratio [RR], 0.89; 95% CI, 0.78–1.01; very low certainty), including in adults identified at higher PPC risk (RR, 0.91; 95% CI, 0.77–1.07; very low certainty). No intervention approach was identified as superior, and no significant benefit was demonstrated when comparing: 1) CPAP (RR, 0.90; 95% CI, 0.79–1.04; very low certainty), 2) NIV (RR, 0.68; 95% CI, 0.41–1.13; very low certainty), 3) continuous NIV/CPAP (RR, 0.90; 95% CI, 0.77–1.05; very low certainty), or 4) intermittent NIV/CPAP (RR, 0.66; 95% CI, 0.39–1.10; very low certainty) to standard care.

CONCLUSIONS:
These findings suggest routine provision of either prophylactic NIV or CPAP following upper abdominal surgery may not be effective to reduce PPCs‚ including in those identified at higher risk.
Is less more in the surgical treatment of early-stage cervical cancer?
Authors: Schaafsma Mirte , Plante Marie , Mom Constantijne H. , van Trommel Nienke E. 
Published: July 2022

Purpose of review
This article discusses recent developments towards less radical surgical treatment for early-stage cervical cancer.

Recent findings
Surgery is the standard treatment for early-stage cervical cancer. In the last decades, new treatment strategies have been developed aiming to reduce morbidity, without hampering oncological safety. We provide an update of the latest knowledge on safety and morbidity following less radical surgical procedures in early-stage cervical cancer. In cervical cancer with a tumour size of 2 cm or less, radical surgery (simple hysterectomy or fertility-sparing conisation) may be a well tolerated option. For patients with larger lesions (>2 cm) and wishing to preserve fertility, administration of neoadjuvant chemotherapy followed by less extensive surgery appears to be a feasible and well tolerated alternative to abdominal trachelectomy. With regard to lymph node assessment, increasing evidence shows the feasibility of the sentinel lymph node procedure instead of full pelvic lymphadenectomy. Prospective trials reporting on oncological safety are awaited.
It is important to exercise caution when new surgical strategies are introduced. Despite promising retrospective data, prospective randomized studies may present unexpected results, for instance, minimally invasive radical hysterectomy showed inferior results compared to laparotomy.

Summary
There is a shift towards less radical treatment for early-stage cervical cancer. This review explores whether and when less is really more.
T-cell-engaging antibodies for the treatment of solid tumors: challenges and opportunities
Authors: Baeuerle Patrick A. , Wesche Holger 
Published: July 2022

Purpose of review
T-cell-engaging antibodies or T-cell engagers (TCEs) can connect a patient's cytotoxic T cells with cancer cells, leading to potent redirected lysis. Until very recently, only one TCE was approved, the CD19/CD3-bispecific blinatumomab. Many new TCEs in late-stage clinical development target various hematopoietic lineage markers like CD20, BCMA, or CD123. Although very compelling single-agent activity of TCEs was observed with various blood-borne cancers, therapy of solid tumor indications has thus far been less successful.

Recent findings
The approval in 2022 of the gp100 peptide-major histocompatibility complex (MHC)/CD3 bispecific TCE tebentafusp in uveal melanoma confirms that TCEs can also efficiently work against solid tumors. TCEs targeting peptide–MHC complexes will expand the target space for solid tumor therapy to intracellular targets. Likewise, early clinical trial data from TCEs targeting DLL3 in small cell lunger cancer showed promising antitumor activity. Various technologies for conditional activation of TCEs in the tumor microenvironment (TME) may expand the scope of conventional surface targets that suffer from a narrow therapeutic window. Finally, pharmacological enhancements for TCE therapies by engagement of certain costimulatory receptors and cytokines, or blockade of checkpoints, are showing promise.

Summary
Targeting peptide–MHC complexes, conditional TCE technologies, and concepts enhancing TCE-activated T cells are paving the way towards overcoming challenges associated with solid tumor therapy.
Incorporation of the UGRAFT Technique to High-definition Liposuction
Authors: Flores González Emmanuel Armando , Viaro Mauricio S. S. , Duran Vega Hector Cesar , Ramírez Guerrero Oliver René , Brito Toledo Patricia , Vázquez Apodaca Raquel Aracely , Rendon Jaramillo Lenin 
Published: July 2022

Summary:
High-definition liposuction is now a reliable procedure that provides more athletic results. It is a trend among plastic surgeons and patients. The ultrasound-guided rectus abdominis fat transfer (UGRAFT) technique has expanded the range of patients who can benefit from rectus abdominis fat grafting, including those without skin laxity. Its advantage over isolated high-definition liposuction is a more natural-looking result because it increases muscle volume and provides a contoured abdomen even during movement, regardless of the patient’s position. In this article, we describe one patient undergoing the UGRAFT technique after high-definition liposuction, versus one patient undergoing only high-definition liposuction. We determined that the use of the UGRAFT technique provides greater muscle definition over those in which this technique has not been performed. The UGRAFT technique opens the possibility of developing more complete body structures regarding definition, providing volume to muscular areas. The more muscle mass and less body fat, the greater the body definition in a liposuction. The less muscle mass and more body fat, the less definition a patient will have in a liposuction. Under these principles, we improve the result by increasing the volume of muscle mass.
Peripheral arterial disease and hypertension
Authors: Gupta Aashish , Patel Rajan A.G. 
Published: July 2022

Purpose of review
Hypertension (HTN) is a well known risk factor for atherosclerosis and peripheral arterial disease (PAD). PAD affects more than 250 million people globally and is associated with worse clinical outcomes. Although multiple studies have been performed to evaluate treatment of HTN in patients with PAD, blood pressure management in this high-risk cohort remains poor.

Recent findings
There has been conflicting evidence regarding blood pressure goals in PAD with some recent studies showing adverse outcomes with low blood pressure in this patient population. Current guidelines, however, continue to recommend treatment goals in PAD patients similar to patients without PAD. To date, no single antihypertensive drug class has shown a clear benefit in PAD population over other antihypertensive drug classes.

Summary
Prospective randomized trials enrolling PAD patients are required that can shed light on optimum blood pressure target and also distinguish between different antihypertensive drugs in terms of reducing adverse outcomes.
Role of advanced imaging with cardiac computed tomography and MRI in atrial and ventricular ablation
Authors: Morris Michael F. , Carlson Chelsea , Bhagat Abhishek 
Published: July 2022

Purpose of review
Increasing evidence supports the use of advanced imaging with cardiac computed tomography (CCT) and cardiac magnetic resonance (CMR) in the work-up of patients with arrythmias being considered for ablation.

Recent findings
Advances in imaging technology and postprocessing are facilitating the use of advanced imaging before, during and after ablation in patients with both atrial and ventricular arrhythmias.
In atrial arrythmias, quantitative assessment of left atrial wall thickness on CCT and quantification of late gadolinium enhancement (LGE) on CMR identify patients more likely to develop recurrent atrial arrythmias following ablation. In addition, in patients with recurrent arrythmia post ablation, LGE CMR can potentially identify targets for repeat ablation.
In ventricular arrythmias, qualitative assessment of LGE can aide in determining the optimal ablation approach and predicts likelihood of ventricular arrythmias inducibility. Quantitative assessment of LGE can identify conduction channels that can be targeted for ablation. On CCT, quantitative assessment of left ventricular wall thickness can demonstrate myocardial ridges associated with re-entrant circuits for ablation.

Summary
This review focuses on the utility of CCT and CMR in identifying key anatomical components and arrhythmogenic substrate contributing to both atrial and ventricular arrhythmias in patients being considered for ablation. Advanced imaging has the potential to improve procedural outcomes, decrease complications and shorten procedural time.