bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes
Authors: Liu Lei , Yang Yu , Deng Yu , Zhang Tong 
Published: December 2022

Abstract
Background
The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing.

Results
Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome.

Conclusions
Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem.
Changing attitudes towards psychotherapy via social observations: are similarities more important than discrepancies?
Authors: Braun-Koch Kristina , Rief Winfried , Teige-Mocigemba Sarah 
Published: December 2022

Abstract
Objectives:
Therapy expectations and attitudes towards psychotherapy contribute substantially to the outcome, process and duration of psychotherapy. The a priori use of role model videos seems to be promising for changing expectations and attitudes towards psychotherapy. In contrast, underlying mechanisms, like identifying with the role model, have been sparsely investigated in studies so far. For instance, the effects of similarities and differences between the role model and the observer are not clear yet.

Methods:
A total of 158 persons were recruited and randomly assigned to four groups. In one of three experimental groups, participants watched an expectation-optimised video with patients giving information about their mostly positive therapy outcomes (positive model). Two further experimental groups saw the same video, but either received instructions to focus on similarities (similarity group) or on differences (discrepancy group) between the patients and themselves. A further control group watched a video with patients who gave information about their symptoms. As the primary outcome variable, we assessed attitudes towards psychotherapy using the Questionnaire on Attitudes towards Psychotherapy (QAPT). It was filled in before and after watching the video and after a two-week follow-up period.

Results:
Contrary to the hypotheses, the discrepancy group and the experimental group without further intervention (positive model) showed significant improvements in their attitudes towards psychotherapy after watching the video, while such an effect was not found in the similarity group or control group.

Conclusion:
Focusing on similarities between patient examples and the observer does not support a change in therapy expectations or attitudes through observation, while a positive video model without instructions, or with the instruction to focus on differences does. Attentional interference and depth of cognitive evaluation are discussed as possible reasons.

Trial registration:
Ethical approval (2018-19k) was obtained from the ethics committee of the Psychological Department, University of Marburg, and the trial was registered at Aspredicted.org (#22,205; 16.04.2019).
Near-field infrared nanoscopic study of EUV- and e-beam-exposed hydrogen silsesquioxane photoresist
Authors: Kim Jiho , Lee Jin-Kyun , Chae Boknam , Ahn Jinho , Lee Sangsul 
Published: December 2022

AbstractThis article presents a technique of scattering-type scanning near-field optical microscopy (s-SNOM) based on scanning probe microscopy as a nanoscale-resolution chemical visualization technique of the structural changes in photoresist thin films. Chemical investigations were conducted in the nanometer regime by highly concentrated near-field infrared on the sharp apex of the metal-coated atomic force microscopy (AFM) tip. When s-SNOM was applied along with Fourier transform infrared spectroscopy to characterize the extreme UV- and electron-beam (e-beam)-exposed hydrogen silsesquioxane films, line and space patterns of half-pitch 100, 200, 300, and 500 nm could be successfully visualized prior to pattern development in the chemical solutions. The linewidth and line edge roughness values of the exposed domains obtained by s-SNOM were comparable to those extracted from the AFM and scanning electron microscopy images after development. The chemical analysis capabilities provided by s-SNOM provide new analytical opportunities that are not possible with traditional e-beam-based photoresist measurement, thus allowing information to be obtained without interference from non-photoreaction processes such as wet development.
Injectable PTHF-based thermogelling polyurethane implants for long-term intraocular application
Authors: Zhang Kaiwen , Liu Zengping , Lin Qianyu , Boo Yi Jian , Ow Valerie , Zhao Xinxin , Wong Daniel Soo Lin , Lim Jason Y. C. , Xue Kun , Su Xinyi , Wu Decheng , Loh Xian Jun 
Published: December 2022

Abstract

Background
Hydrogels show great potential to be used for intraocular applications due to their high-water content and similarity to the native vitreous. Injectable thermosensitive hydrogels through a small-bore needle can be used as a delivery system for drugs or a tamponading substitute to treat posterior eye diseases with clear clinical potential. However, none of the currently available thermosensitive hydrogels can provide intraocular support for up to 3 months or more.

Method
In this study, an injectable polytetrahydrofuran (PTHF)-based thermosensitive hydrogel was synthesized by polyurethane reaction. We examined the injectability, rheological properties, microstructure, cytotoxicity, and in vivo compatibility and stability of the hydrogels in rabbit eyes.

Results
We found that the PTHF block type and PTHF component ratio could modulate thermogelation properties of the polyurethane polymers. The PTHF-based hydrogel implants retained normal retinal structure and function. Incorporating bioinert PTHF generated highly biocompatible and more stable thermogels in the vitreous cavity, with gel networks and the presence of polymer still observed after 3 months when other thermogels would have been completely cleared. Moreover, despite lacking hydrolytically cleavable linkages, the polymers could be most naturally removed from the native vitreous by bio-erosion without additional surgical interventions.

Conclusion
Our findings suggest the potential of incorporating hydrophobic bioinert blocks to enhance the in vivo stability of supramolecularly associated hydrogels for long-term intraocular applications.

Graphical Abstract
PEG-mediated transduction of rAAV as a platform for spatially confined and efficient gene delivery
Authors: Zou Liang , Wang Jinfen , Fang Ying , Tian Huihui 
Published: December 2022

Abstract

Background
Recombinant adeno-associated viruses (rAAV) are commonly used vectors for gene delivery in both basic neuroscience and clinical applications due to their nonpathogenic, minimally immunogenic, and sustained expression properties. However, several challenges remain for the wide-scale rAAV applications, including poor infection of many clinically important cell lines, insufficient expression at low titers, and diffusive transduction in vivo.

Methods
In this work, PEG, which is a safe and non-toxic polymer of ethylene oxide monomer, was applied as an auxiliary transduction agent to improve the expression of rAAV. In detail, a small dose of PEG was added into the rAAV solution for the transgene expression in cell lines in vitro, and in the central nervous system (CNS) in vivo. The biocompatibility of PEG enhancer was assessed by characterizing the immune responses, cell morphology, cell tropism of rAAV, neuronal apoptosis, as well as motor function of animals.

Results
The results show that small dose of PEG additive can effectively improve the gene expression characteristics of rAAV both in vitro and in vivo. Specifically, the PEG additive allows efficient transgene expression in cell lines that are difficult to be transfected with rAAV alone. In vivo studies show that the PEG additive can promote a spatially confined and efficient transgene expression of low-titer rAAV in the brain over long terms. In addition, no obvious side effects of PEG were observed on CNS in the biocompatibility studies.

Conclusions
This spatially confined and efficient transduction method can facilitate the applications of rAAV in fundamental research, especially in the precise dissection of neural circuits, and also improve the capabilities of rAAV in the treatment of neurological diseases which originate from the disorders of small nuclei in the brain.
Intradural extramedullary cervical metastasis from Merkel cell carcinoma: a case report and literature review
Authors: Pennisi Giovanni , Talacchi Andrea , Tirendi Marcello Nunzio , Giordano Marco , Olivi Alessandro 
Published: December 2022

Abstract
Background
Merkel cell carcinoma (MCC) is a rare aggressive primary skin carcinoma with an incidence of 44 cases per 100,000.
The natural course of MCC often results in rapid growth and early metastasis. On the other hand, the spinal cord is rarely affected and frequently features the end stage of the disease. The aim of this paper was to clarify the management of patients with spine metastasis from a skin lesion and showed a case-based update.

Case presentation
A 73-year-old female was admitted to the Neurosurgical Department in December 2021 for a sudden right hemiparesis with bladder dysfunction and a history of cutaneous Merkel cell carcinoma. A magnetic resonance imaging (MRI) of the central nervous system (CNS) showed an intradural-extramedullary right-sided C6–C7 tumor with mass effect and edema of the cervical cord. The patient underwent a C6–C7 laminectomy with microsurgical total resection of the intradural extramedullary lesion. The neuropathological examination identified a metastasis from Merkel cell carcinoma. Nowadays, evidence for spinal metastasis from malignities skin cancer is generally lacking, probably because they are extremely rare. The exact time of life expectancy is controversial, and some clinicians use a cutoff of 3 months to determine whether surgical intervention should be offered, while others advocate at least 6 months of life expectancy.

Conclusions
To the best of our knowledge, we showed the first case of solitary intradural extramedullary cervical spine metastasis from MCC. We recommend to consider metastasis of MCC in the differential diagnosis of spinal metastasis.
Characteristics of the 6th Japanese wave of COVID-19 in hemodialysis patients
Authors: Haruta Munenori , Otsubo Shigeru , Otsubo Yuriko 
Published: December 2022

AbstractBackgroundWe examined the clinical characteristics of hemodialysis patients with COVID-19 during the 6th wave of infection (mainly Omicron variant) in Japan.MethodsHemodialysis patients admitted in January 2022 and thereafter were grouped as the 6th wave group (n = 53), while others were grouped as the 1st–5th wave group (n = 47).ResultsThe proportion of vaccinations was significantly higher in the 6th wave group than in the 1st–5th wave group (96.2% vs 10.6%,p < 0.0001). Neutralizing antibody and molnupiravir were used more frequently in the 6th wave group (75.5% and 88.7%) than in the 1st–5th wave group (14.9% and 0%, bothp < 0.0001). The critical disease was seen in 21.3% of the patients in the 1st–5th wave group and 0% in the 6th wave group (p < 0.001).ConclusionThe prognosis of hemodialysis patients in the 6th wave group was good. The vaccination and advances in the treatment may have contributed to the outcomes.
A simple and automated method for 161Tb purification and ICP-MS analysis of 161Tb
Authors: McNeil Scott W. , Van de Voorde Michiel , Zhang Chengcheng , Ooms Maarten , Bénard François , Radchenko Valery , Yang Hua 
Published: December 2022

Abstract
Background
161Tb is a radiolanthanide with the potential to replace 177Lu in targeted radionuclide therapy. 161Tb is produced via the neutron irradiation of [160Gd]Gd2O3 targets, and must be purified from 160Gd and the decay product 161Dy prior to use. Established purification methods require complex conditions or high-pressure ion chromatography (HPIC) which are inconvenient to introduce in a broad user community. This study aims to find a simpler small solid-phase extraction (SPE) column method for 161Tb purification that is more suitable for automation with commercially available systems like TRASIS.

Results
We first tested the distribution coefficients on TK211 and TK212 resins for the separation of Gd, Tb, and Dy, and subsequently developed a method to separate these metal ions, with an additional TK221 resin to concentrate the final product. A side-by-side comparison of the products purified using this new method with the HPIC method was undertaken, assessing the radionuclidic purity, chemical purity regarding Gd and Dy, and labeling efficiency with a standard chelate (DOTA) and a novel chelate (crown). The two methods have comparable radionuclidic purity and labeling efficiency. The small SPE column method reduced Gd content to nanogram level, although still higher than the HPIC method. An ICP-MS method to quantify 161Tb, 159Tb, 160Gd, and 161Dy was developed with the application of mass-shift by ammonia gas. Last, 161Tb produced from the small SPE column method was used to assess the biodistribution of [161Tb]Tb-crown-αMSH, and the results were comparable to the HPIC produced 161Tb.

Conclusions
161Tb was successfully purified by a semi-automated TRASIS system using a combination of TrisKem extraction resins. The resulting product performed well in radiolabelling and in vivo experiments. However, improvement can be made in the form of further reduction of 160Gd target material in the final product. An ICP-MS method to analyze the radioactive product was developed. Combined with gamma spectroscopy, this method allows the purity of 161Tb being assessed before the decay of the product, providing a useful tool for quality control.
Elementary math in elementary school: the effect of interference on learning the multiplication table
Authors: Dotan Dror , Zviran-Ginat Sharon 
Published: December 2022

AbstractMemorizing the multiplication table is a major challenge for elementary school students: there are many facts to memorize, and they are often similar to each other, which creates interference in memory. Here, we examined whether learning would improve if the degree of interference is reduced, and which memory processes are responsible for this improvement. In a series of 16 short training sessions over 4 weeks, first-grade children learned 16 multiplication facts—4 facts per week. In 2 weeks the facts were dissimilar from each other (low interference), and in 2 control weeks the facts were similar (high interference). Learning in the low-similarity, low-interference weeks was better than in the high-similarity weeks. Critically, this similarity effect originated in the specific learning context, i.e., the grouping of facts to weeks, and could not be explained as an intrinsic advantage of certain facts over others. Moreover, the interference arose from the similarity between facts in a given week, not from the similarity to previously learned facts. Similarity affected long-term memory—its effect persisted 7 weeks after training has ended; and it operated on long-term memory directly, not via the mediation of working memory. Pedagogically, the effectiveness of the low-interference training method, which is dramatically different from currently used pedagogical methods, may pave the way to enhancing how we teach the multiplication table in school.
Patient and healthcare provider perceptions on using patient-reported experience measures (PREMs) in routine clinical care: a systematic review of qualitative studies
Authors: Shunmuga Sundaram Chindhu , Campbell Rachel , Ju Angela , King Madeleine T. , Rutherford Claudia 
Published: December 2022

Abstract
Background
Patient-reported experience measures (PREMs) assess quality-of-care from patients’ perspectives. PREMs can be used to enhance patient-centered care and facilitate patient engagement in care. With increasing quality improvement studies in clinical practice, the use of PREMs has surged. As a result, knowledge about stakeholder experiences of using PREMs to assess quality of care across diverse clinical settings is needed to inform PREM implementation efforts. To address this, this review examines the qualitative literature on patient and healthcare provider experiences of using PREMs in clinical practice.

Methods
Medline, Embase and PsycInfo were systematically searched from inception to May 2021. Additional searching of reference lists for all included articles and relevant review articles were performed. Retrieved articles were screened for eligibility by one reviewer and 25% cross-checked by a second reviewer across all stages of the review. Full texts meeting eligibility criteria were appraised against the COREQ checklist for quality assessment and thematic analysis was used to analyze textual data extracted from the results.

Results
Electronic searches identified 2683 records, of which 20 studies met eligibility criteria. Extracted data were synthesized into six themes: facilitators to PREM implementation; barriers to PREM implementation; healthcare providers’ perspectives towards using PREMs; patients’ perspectives towards using PREMs; advantages of using PREMs in clinical practice; limitations and practical considerations to reduce resistance of PREM usage. The primary factors facilitating and impeding the use of PREMs include organizational-, staff- and patient-related factors.

Conclusion
Results can be used to guide the usage and implementation of PREMs in clinical settings by addressing the identified barriers and building on the perceived benefits to encourage adoption of PREMs. Results around facilitators to PREM implementation and practical considerations could also promote appropriate use of PREMs by healthcare providers, helping to improve practice and the quality of care based on patient feedback.
Performance of door-to-CT time of code stroke in Indonesian tertiary referral center hospital
Authors: Rasyid Al , Kurniawan Mohammad , Mesiano Taufik , Hidayat Rakhmad , Rilianto Beny , Harris Salim 
Published: December 2022

Abstract
Background
This study was aimed to analyze the performance of door-to-CT scan (DTC) time of code stroke at the central referral hospital in Indonesia. Data from 310 patients were obtained in this cross-sectional study. Inclusion criteria were: notified with code stroke within the period between November 2016 and April 2019. Bivariate and multivariate analyses were carried out to find which factors affecting DTC time.

Results
A tendency of decreasing DTC time was reported from November 2016 until April 2019. The median DTC time at study endpoint was 19.5 (1–210) minutes. Chi-square analysis showed that CT scan location was the factor associated with DTC (OR: 12.6, 95% CI 6.8–23.35, p < 0.001). Logistic regressions analysis also showed significant relationship of CT scan location and DTC (OR: 24.27, 95% CI 17.71–30.81, p < 0.05).

Conclusions
Refinement of the code stroke implementation and CT scan placement in the Emergency Department (ED) are effective in reduction of DTC time, and as a result, improving acute stroke management.
Comparison of thoracic epidural and thoracic erector spinae plane block for pain relief of posterolateral rib fractures—a retrospective cohort study
Authors: Diwan Sandeep Madhusudan , Adhye Bharati , Nair Abhijit , Sancheti Parag 
Published: December 2022

Abstract
Background
Pain from rib fractures (posterior/lateral/anterior) is associated with significant pulmonary morbidity. Earlier epidural and paravertebral blocks were implemented in the algorithm for multimodal pain management of rib fracture pain. Administration of these blocks are fraught with challenges encountered in intensive care unit (ICU). The erector spinae plane block (ESPB) is a viable alternative in ICU set up.
This retrospective study compared continuous thoracic ESPB and continuous thoracic epidural analgesia (TEA) [n=28 versus n=24] for polytrauma patients who sustained unilateral multiple rib fractures (MRFs), i.e., more than 3 admitted in ICU. Demography data were noted and compared. Outcome measures were block efficacy in terms of pain scores, opioid consumption (intravenous fentanyl), technical difficulties, and complications.

Results
Age, gender, and sides of ribs fractures were comparable in all groups. Pain scores and fentanyl consumption were significantly better in patients who received TEA.

Conclusions
Though statistically significant analgesic efficacy was observed with continuous TEA for managing pain due to unilateral posterolateral MRFs, the small sample size was a major limitation. Further prospective comparative study including effects on incentive spirometry and effectiveness of chest physiotherapy is warranted. However, continuous ESPB is simple and safe to perform with few theoretical contraindications.