bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanobodies as novel potential drugs to target cardiac light chain amyloidosis
Authors: Broggini L , Giono M , Speranzini V , Barzago MM , Palladini G , Diomede L , Pappone C , Ricagno S 
Published: June 2022

Abstract

Funding Acknowledgements
Type of funding sources: Private hospital(s). Main funding source(s): IRCCS GRUPPO SAN DONATO
Light chain amyloidosis (AL) is a systemic disease where fibrillar deposition of misfolded immunoglobulin light chains (LCs) severely affects organ functions. Cardiac involvement (75% of all AL cases) results in the worst prognosis for patients (1). Current AL therapies rely on repurposing of chemotherapeutic drugs targeting plasma cells as the source of LCs; however patients with cardiac damage are often too compromised to sustain such regiments. Alternative approaches aimed at destroying AL fibrils are being evaluated in clinical trials. Nevertheless, none of these treatments offer reliable solutions to counteract the life-threatening cardiac involvement in AL (2).
Here, we propose an alternative approach targeting soluble toxic LCs: these immunoglobulin fragments are frequently overexpressed in patients with cardiac damage and have been found to exert toxicity to cardiac cells, making them an ideal candidate as new drug targets for cardiac AL (3). We combined a multidisciplinary approach to scout for and probe next generation AL drugs based on nanobodies designed to specifically bind soluble toxic LCs. Compared to conventional monoclonal antibodies, nanobodies consist of just two heavy chains, with a single variable domain (VHH, ~15kDa) as the antigen-binding region. These nanoscale VHHs can retain full antigen-binding potential upon isolation, establishing them as the smallest, naturally-derived antigen-binding fragment (4).
To reach our aim, 11 different nanobodies against a cardiotoxic light chain (H3), derived from patient suffering from AL (5), were produced and characterized. To identify the most promising among the pool, a detailed characterization of the in vitro binding between H3 and each nanobody was performed, using a series of biophysical techniques, including isothermal titration calorimetry, microscale thermophoresis, bio-layer interferometry, and multi-angle light scattering. Notably, all the nanobodies efficiently bind to H3 forming stable complexes.
Then, to investigate the capability of nanobodies to prevent H3 cardiotoxicity, we used the nematode C. elegans as in vivo model. Indeed, in C. elegans the administration of cardiotropic LCs causes a profound functional and structural damage on the pharynx, considered an "ancestral heart" (6). Interestingly, we found that some of our nanobodies prevented H3 from exerting its toxic activity, as their presences preserve nematode functional parameters. Collectively, our data pinpointed the novel potential role of nanobodies in the development of alternative treatments of AL patients with cardiac involvement.
The Last Voyage of the Gloucester (1682): The Politics of a Royal Shipwreck
Authors: Jowitt Claire 
Published: June 2022

Abstract
The significance of the wreck of the Gloucester on 6 May 1682 en route to Scotland, with James Stuart, duke of York, later James II and VII, on board, is poorly understood. Based on new archival research, this article places the event in its political, cultural and naval contexts in order to re-evaluate its importance to British history and to correct a number of inaccuracies in recent historiography. The wreck occurred at a sensitive political moment when, within the maelstrom of the Exclusion Crisis (1679–81), the Duke was hopeful of securing his place in the succession. However, thanks in part to the cultural vigour of the ‘ship of state’ trope, the disaster risked James being regarded as a pilot and commander unable to steer the nation. Because his political enemies could use the shipwreck as propaganda to undermine his position as heir to the throne, the event in general, and especially the Duke’s behaviour, became popular topics which were debated and contested from Whig and Tory viewpoints. Since the tragedy occurred at sea, one arm of early modern state apparatus that was especially responsive to these debates was the English navy, which was itself in the midst of a power struggle between Crown and admiralty for control over its future direction. The article sheds new light on the far-reaching implications for James’s reign of the sinking of the Gloucester, and argues afresh for the centrality of maritime history to Restoration political history.
The ecological roles of assembling genomes for Bacillales and Clostridiales in coal seams
Authors: Li Yang , Liu Bingjun , Tu Qingyi , Xue Sheng , Liu Xiaozhou , Wu Zhijian , An Shikai , Chen Jian , Wang Zhigen 
Published: June 2022

AbstractBiogenic coalbed methane is produced by biological processes mediated by synergistic interactions of microbial complexes in coal seams. However, the ecological role of functional bacteria in biogenic coalbed methane remains poorly understood. Here, we studied the metagenome assembled genomes (MAGs) of Bacillales and Clostridiales from coal seams, revealing further expansion of hydrogen and acetogen producers involved in organic matter decomposition. In this study, Bacillales and Clostridiales were dominant orders (91.85 ± 0.94%) in cultured coal seams, and a total of 16 MAGs from six families, including Bacillus, Paenibacillus, Staphylococcus, Anaerosalibacter, Hungatella and Paeniclostridium, were reconstructed. These microbial groups possessed multiple metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate, β-oxidation, TCA cycle, assimilatory sulfate reduction, nitrogen metabolism and encoding hydrogenase) that provided metabolic substrates (acetate and/or H2) for the methanogenic processes. Therein, the hydrogenase-encoding gene and hydrogenase maturation factors were merely found in all the Clostridiales MAGs. β-oxidation was the main metabolic pathway involved in short-chain fatty acid degradation and acetate production, and most of these pathways were detected and exhibited different operon structures in Bacillales MAGs. In addition, assimilatory sulfate reduction and nitrogen metabolism processes were also detected in some MAGs, and these processes were also closely related to acetate production and/or organic matter degradation according to their operon structures and metabolic pathways. In summary, this study enabled a better understanding of the ecological roles of Bacillales and Clostridiales in biogenic methane in coal seams based on a combination of bioinformatic techniques.
Contribution of the Root Component to Soil Respiration in Oriental Beech Stands in Artvin, Turkey
Authors: Akbas Musa , Tufekcioglu Aydın 
Published: June 2022

Abstract
Autotrophic (root) and heterotrophic respiration components respond differently to environmental variables, and each component behaves differently at different time scales, so it is necessary to partition total soil respiration into its components. The aims of this study were determine soil respiration and its root and heterotrophic components in beech stands, examine the relationship between respiration and biogeochemical factors, and assess seasonal variation in soil respiration. Trenching was applied to separate soil respiration components 6 months before measurements. Monthly soil respiration, temperature and moisture measurements, and seasonal soil and root sampling were carried out in Oriental beech (Fagus orientalis L.) stands located in Artvin Saçinka, Turkey from April 2018 to November 2018 and also (except soil sampling) from May 2019 to November 2019. The average contribution of root respiration and heterotrophic respiration to total soil respiration were 58.8% and 41.2%, respectively. Carbon and nitrogen dynamics explained variations of soil respiration with significant models. This study indicates that soil respiration and its components are associated with biogeochemical factors as well as environmental climatic conditions, and each component of respiration responds differently to changes in them.
On a Continuous Sárközy-Type Problem
Authors: Kuca Borys , Orponen Tuomas , Sahlsten Tuomas 
Published: June 2022

Abstract
We prove that there exists a constant $\epsilon&gt; 0$ with the following property: if $K \subset {\mathbb {R}}^2$ is a compact set that contains no pair of the form $\{x, x + (z, z^{2})\}$ for $z \neq 0$, then $\dim _{\textrm {H}} K \leq 2 - \epsilon $.
Green Liquid Chromatography Method for the Determination of Related Substances Present in Olopatadine HCl Nasal Spray Formulation, Robustness by Design Expert
Authors: Kowtharapu Leela Prasad , Katari Naresh Kumar , Sandoval Christian A , Muchakayala Siva Krishna , Rekulapally Vijay Kumar 
Published: June 2022

Abstract

Background
Dual therapeutic nature drug mast cell stabilizer and histamine receptor antagonist olopatadine hydrochloride (OPT) nasal spray does not have an official monograph, and no literature is available. Eye drops formulation had the official monograph for impurities, but the determination was done in two methods.

Objective
A simple and effective green liquid chromatography method to develop and validate for the related substances of OPT nasal spray formulation.

Method
A 25 min gradient method was employed to separate impurities and OPT with a 1.0 mL/min flow rate using a Boston green C8 (150 mm × 4.6 mm, 5 µm) HPLC column. The set wavelength and column oven temperatures were 299 nm and 30°C, respectively. pH 3.5 phosphate buffer–acetonitrile in the ratio of (70:30, v/v) as mobile phase A and (50:50, v/v) ratio as mobile phase B. A Quality by Design (QbD) based Design of Experiments (DoE) was employed to evaluate the robustness characteristics of the analytical method validation.

Results
The obtained RSD from the precision and intermediate precision was 0.4 to 4.1%. The % recovery of the impurities from LOQ to 150% of specification level was 87.5 to 110.3%. The linear regression curves for the impurities with a correlation coefficient of &gt;0.999 indicate that all peak responses are linear with the concentration. The sample and standard solutions were stable for 24 h at benchtop and refrigerator conditions.

Conclusions
All the critical peaks were well separated from the forced degradation studies’ diluent, placebo, and generated degradation peaks. The method validation data and QbD based robustness study results indicate that the developed impurities method fits the routine quality control laboratory use. National Environmental Index (NMEI), Green Analytical Procedure Index (GAPI), Analytical Eco-scale and Analytical Greenness (AGREE) tools expressed the method’s greenness.

Highlights
The proposed method is QbD utilized and green chemistry assessed impurities determination method for OPT in nasal spray formulation.
Peroneus longus intra-tendinous ganglion cyst
Authors: Khoja Yousef Tawfik , Altammami Abdulaziz Fahad , Alattas Mohammed Hashem 
Published: June 2022

Abstract
Ganglion cysts arising from tendons are uncommon lesions with an unknown cause. We present a case report of a 38-year-old female was diagnosed with an intra-tendinous ganglion cyst of the peroneus longus. She complained of right ankle swelling for 1 year and associated with pain. MRI revealed a peroneus longus intra-tendinous ganglion below the lateral malleolus with a thin wall. The ganglion cyst was surgically excised while the structure of the peroneus longus tendon was preserved. The clinical and functional outcomes were satisfactory after 1 year without recurrence.
Vectorial folding of telomere overhang promotes higher accessibility
Authors: Paul Tapas , Opresko Patricia L , Ha Taekjip , Myong Sua 
Published: June 2022

Abstract
Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5′ to 3′) and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5′ to 3′ direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.
Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA
Authors: Mair Stefan , Erharter Kevin , Renard Eva , Brillet Karl , Brunner Melanie , Lusser Alexandra , Kreutz Christoph , Ennifar Eric , Micura Ronald 
Published: June 2022

Abstract
Nucleobase deamination, such as A-to-I editing, represents an important posttranscriptional modification of RNA. When deamination affects guanosines, a xanthosine (X) containing RNA is generated. However, the biological significance and chemical consequences on RNA are poorly understood. We present a comprehensive study on the preparation and biophysical properties of X-modified RNA. Thermodynamic analyses revealed that base pairing strength is reduced to a level similar to that observed for a G•U replacement. Applying NMR spectroscopy and X-ray crystallography, we demonstrate that X can form distinct wobble geometries with uridine depending on the sequence context. In contrast, X pairing with cytidine occurs either through wobble geometry involving protonated C or in Watson–Crick-like arrangement. This indicates that the different pairing modes are of comparable stability separated by low energetic barriers for switching. Furthermore, we demonstrate that the flexible pairing properties directly affect the recognition of X-modified RNA by reverse transcription enzymes. Primer extension assays and PCR-based sequencing analysis reveal that X is preferentially read as G or A and that the ratio depends on the type of reverse transcriptase. Taken together, our results elucidate important properties of X-modified RNA paving the way for future studies on its biological significance.
ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia
Authors: Lao Linjiang , Bourdeau Isabelle , Gagliardi Lucia , He Xiao , Shi Wei , Hao Bingbing , Tan Minjia , Hu Yan , Peng Junzheng , Coulombe Benoit , Torpy David J , Scott Hamish S , Lacroix Andre , Luo Hongyu , Wu Jiangping 
Published: June 2022

Abstract
ARMC5 is implicated in several pathological conditions, but its function remains unknown. We have previously identified CUL3 and RPB1 (the largest subunit of RNA polymerase II (Pol II) as potential ARMC5-interacting proteins. Here, we show that ARMC5, CUL3 and RBX1 form an active E3 ligase complex specific for RPB1. ARMC5, CUL3, and RBX1 formed an active E3 specific for RPB1. Armc5 deletion caused a significant reduction in RPB1 ubiquitination and an increase in an accumulation of RPB1, and hence an enlarged Pol II pool in normal tissues and organs. The compromised RPB1 degradation did not cause generalized Pol II stalling nor depressed transcription in the adrenal glands but did result in dysregulation of a subset of genes, with most upregulated. We found RPB1 to be highly expressed in the adrenal nodules from patients with primary bilateral macronodular adrenal hyperplasia (PBMAH) harboring germline ARMC5 mutations. Mutant ARMC5 had altered binding with RPB1. In summary, we discovered that wildtype ARMC5 was part of a novel RPB1-specific E3. ARMC5 mutations resulted in an enlarged Pol II pool, which dysregulated a subset of effector genes. Such an enlarged Pol II pool and gene dysregulation was correlated to adrenal hyperplasia in humans and KO mice.
Identifying ribosome heterogeneity using ribosome profiling
Authors: Alkan Ferhat , Wilkins Oscar G , Hernández-Pérez Santiago , Ramalho Sofia , Silva Joana , Ule Jernej , Faller William J 
Published: June 2022

Abstract
Recent studies have revealed multiple mechanisms that can lead to heterogeneity in ribosomal composition. This heterogeneity can lead to preferential translation of specific panels of mRNAs, and is defined in large part by the ribosomal protein (RP) content, amongst other things. However, it is currently unknown to what extent ribosomal composition is heterogeneous across tissues, which is compounded by a lack of tools available to study it. Here we present dripARF, a method for detecting differential RP incorporation into the ribosome using Ribosome Profiling (Ribo-seq) data. We combine the ‘waste’ rRNA fragment data generated in Ribo-seq with the known 3D structure of the human ribosome to predict differences in the composition of ribosomes in the material being studied. We have validated this approach using publicly available data, and have revealed a potential role for eS25/RPS25 in development. Our results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new method to study this phenomenon. Furthermore, with dripARF, previously published Ribo-seq data provides a wealth of new information, allowing the identification of RPs of interest in many disease and normal contexts. dripARF is available as part of the ARF R package and can be accessed through https://github.com/fallerlab/ARF.
TBX2 acts as a potent transcriptional silencer of tumour suppressor genes through interaction with the CoREST complex to sustain the proliferation of breast cancers
Authors: McIntyre Alexander J , Angel Charlotte Z , Smith James S , Templeman Amy , Beattie Katherine , Beattie Shannon , Ormrod Alice , Devlin Eadaoin , McGreevy Charles , Bothwell Chloe , Eddie Sharon L , Buckley Niamh E , Williams Rich , Mullan Paul B 
Published: June 2022

AbstractChromosome 17q23 amplification occurs in 20% of primary breast tumours and is associated with poor outcome. The TBX2 gene is located on 17q23 and is often over-expressed in this breast tumour subset. TBX2 is an anti-senescence gene, promoting cell growth and survival through repression of Tumour Suppressor Genes (TSGs), such as NDRG1 and CST6. Previously we found that TBX2 cooperates with the PRC2 complex to repress several TSGs, and that PRC2 inhibition restored NDRG1 expression to impede cellular proliferation. Here, we now identify CoREST proteins, LSD1 and ZNF217, as novel interactors of TBX2. Genetic or pharmacological targeting of CoREST emulated TBX2 loss, inducing NDRG1 expression and abolishing breast cancer growth in vitro and in vivo. Furthermore, we uncover that TBX2/CoREST targeting of NDRG1 is achieved by recruitment of TBX2 to the NDRG1 promoter by Sp1, the abolishment of which resulted in NDRG1 upregulation and diminished cancer cell proliferation. Through ChIP-seq we reveal that 30% of TBX2-bound promoters are shared with ZNF217 and identify novel targets repressed by TBX2/CoREST; of these targets a lncRNA, LINC00111, behaves as a negative regulator of cell proliferation. Overall, these data indicate that inhibition of CoREST proteins represents a promising therapeutic intervention for TBX2-addicted breast tumours.
Real-world Antimicrobial Stewardship Experience in a Large Academic Medical Center: Using Statistical and Machine Learning Approaches to Identify Intervention “Hotspots” in an Antibiotic Audit and Feedback Program
Authors: Goodman Katherine E , Heil Emily L , Claeys Kimberly C , Banoub Mary , Bork Jacqueline T 
Published: June 2022

Abstract

Background
Prospective audit with feedback (PAF) is an impactful strategy for antimicrobial stewardship program (ASP) activities. However, because PAF requires reviewing large numbers of antimicrobial orders on a case-by-case basis, PAF programs are highly resource intensive. The current study aimed to identify predictors of ASP intervention (ie, feedback) and to build models to identify orders that can be safely bypassed from review, to make PAF programs more efficient.

Methods
We performed a retrospective cross-sectional study of inpatient antimicrobial orders reviewed by the University of Maryland Medical Center’s PAF program between 2017 and 2019. We evaluated the relationship between antimicrobial and patient characteristics with ASP intervention using multivariable logistic regression models. Separately, we built prediction models for ASP intervention using statistical and machine learning approaches and evaluated performance on held-out data.

Results
Across 17 503 PAF reviews, 4219 (24%) resulted in intervention. In adjusted analyses, a clinical pharmacist on the ordering unit or receipt of an infectious disease consult were associated with 17% and 56% lower intervention odds, respectively (adjusted odds ratios [aORs], 0.83 and 0.44; P ≤ .001 for both). Fluoroquinolones had the highest adjusted intervention odds (aOR, 3.22 [95% confidence interval, 2.63–3.96]). A machine learning classifier (C-statistic 0.76) reduced reviews by 49% while achieving 78% sensitivity. A “workflow simplified” regression model that restricted to antimicrobial class and clinical indication variables, 2 strong machine learning–identified predictors, reduced reviews by one-third while achieving 81% sensitivity.

Conclusions
Prediction models substantially reduced PAF review caseloads while maintaining high sensitivities. Our results and approach may offer a blueprint for other ASPs.
Severe Libman–Sacks endocarditis complicating antiphospholipid syndrome: a retrospective analysis of 23 operated cases
Authors: Chalvon Nellie Bourse , Costedoat-Chalumeau Nathalie , Pennaforte Jean-Loup , Servettaz Amelie , Boulagnon Rombi Camille , Gavand Pierre-Edouard , Lekieffre Maud , Le Guern Veronique , Morel Nathalie , Cohen Aubart Fleur , Haroche Julien , Mathian Alexis , Collet Jean-Philippe , Piette Jean-Charles , Amoura Zahir , Orquevaux Pauline 
Published: June 2022

Abstract

Objective
Data on severe heart valve disease (HVD), including Libman–Sacks endocarditis, associated with SLE and/or APS requiring valvular surgery are scarce. We thus conducted a retrospective study, aimed at describing and clarifying clinical, laboratory, echocardiographic, histopathological and evolutional features of SLE and/or APS patients with severe associated-HVD.

Methods
An observational retrospective multicentric analysis of 23 adults with SLE and/or APS and HVD between 1996 and 2019 and available histopathological report evaluating long-term follow-up.

Results
Twenty-three individuals (20 females, median age 37 [range 17–76] years) were included. All had APS (thrombotic in 22, with an arterial phenotype in 15 and with catastrophic APS [CAPS] in six), and 11 (47%) had SLE. Systemic underlying disease had been diagnosed prior to HVD in 12 (52%). In 10 patients (43%), HVD was complicated by cerebral stroke prior to surgery. Twenty patients (87%) had only one pathological valve, the mitral valve in 18 patients (78%). Valvular thickening (n = 19) and valvular regurgitation (n = 19) were the most frequently reported lesions. Fifteen (62%) patients underwent mechanical valve replacement, six (26%) conservative valve repair (five were later re-operated after a median time of 1 [0–4] year), and two (9%) underwent biological valve replacement. Nine patients (39%) presented early-onset post-operative complications, including three CAPS immediately after surgery and one death. After surgery, 18 patients (78%) had normal postoperative valvular function, but almost half of the patients (43%) had post-operative neurological sequelae (median follow-up of 6 [2–20] years).

Conclusion
Severe HVD leading to surgery was strongly associated with thrombotic APS, especially arterial phenotypes. Half of the reported patients presented cerebral stroke complicating the HVD. Valvular surgery carried a significant risk of CAPS.