bluuebunny/crossref_metadata_2025_split huggingface dataset:
Split scar sign to predict complete response in rectal cancer after neoadjuvant chemoradiotherapy: systematic review and meta-analysis
Authors: Torri Giovanni Brondani , Wiethan Camila Piovesan , Langer Felipe Welter , de Oliveira Guilherme Strieder , Meirelles Alice Villa Bella , Horvat Natally , Tse Justin Ruey , Dias Adriano Basso , Altmayer Stephan 
Published: November 2023

Abstract
Objectives
Magnetic resonance imaging (MRI) is the modality of choice for rectal cancer initial staging and restaging after neoadjuvant chemoradiation. Our objective was to perform a meta-analysis of the diagnostic performance of the split scar sign (SSS) on rectal MRI in predicting complete response after neoadjuvant therapy.

Methods
MEDLINE, EMBASE, and Cochrane databases were searched for relevant published studies through June 2023. Primary studies met eligibility criteria if they evaluated the diagnostic performance of the SSS to predict complete response on pathology or clinical follow-up in patients undergoing neoadjuvant chemoradiation. A meta-analysis with a random-effects model was used to estimate pooled sensitivity and specificity, area under the curve (AUC), and diagnostic odds ratio (DOR) of the SSS.

Results
A total of 4 studies comprising 377 patients met the inclusion criteria. The prevalence of complete response in the studies was 21.7–52.5%. The pooled sensitivity and specificity of the SSS to predict complete response were 62.0% (95% CI, 43.5–78.5%) and 91.9% (95% CI, 78.9–97.2%), respectively. The estimated AUC for SSS was 0.83 (95% CI, 0.56–0.94) with a DOR of 18.8 (95% CI, 3.65–96.5).

Conclusion
The presence of SSS on rectal MRI demonstrated high specificity for complete response in patients with rectal cancer after neoadjuvant chemoradiation. This imaging pattern can be a valuable tool to identify potential candidates for organ-sparing treatment and surveillance.

Clinical relevance statement
SSS presents high specificity for complete response post-neoadjuvant. This MRI finding enhances rectal cancer treatment assessment and aids clinicians and patients in choosing watch-and-wait over immediate surgery, which can potentially reduce costs and associated morbidity.

Key Points
•Fifteen to 50% of rectal cancer patients achieve complete response after neoadjuvant chemoradiation and may be eligible for a watch-and-wait strategy.
•The split scar sign has high specificity for a complete response.
•This imaging finding is valuable to select candidates for organ-sparing management.
Cytosolic nucleic acid sensing and mitochondrial transcriptomic changes as early triggers of metabolic disease in db/db mice
Authors: Ludwig-Słomczyńska Agnieszka H. , Seweryn Michał T. , Wiater Jerzy , Borys Agnieszka , Ledwoń Anna , Druszczyńska Magdalena , Łabieniec-Watała Magdalena , Lis Grzegorz J. , Wołkow Paweł P. 
Published: November 2023

AbstractAnimal models of diabetes, such as db/db mice, are a useful tool for deciphering the genetic background of molecular changes at the initial stages of disease development. Our goal was to find early transcriptomic changes in three tissues involved in metabolism regulation in db/db mice: adipose tissue, muscle tissue and liver tissue. Nine animals (three per time point) were studied. Tissues were collected at 8, 12 and 16 weeks of age. Transcriptome-wide analysis was performed using mRNA-seq. Libraries were sequenced on NextSeq (Illumina). Differential expression (DE) analysis was performed with edgeR. The analysis of the gene expression profile shared by all three tissues revealed eight upregulated genes (Irf7, Sp100, Neb, Stat2, Oas2, Rtp4, H2-T24 and Oasl2) as early as between 8 and 12 weeks of age. The most pronounced differences were found in liver tissue: nine DE genes between 8 and 12 weeks of age (Irf7, Ly6a, Ly6g6d, H2-Dma, Pld4, Ly86, Fcer1g, Ly6e and Idi1) and five between 12 and 16 weeks of age (Irf7, Plac8, Ifi44, Xaf1 and Ly6a) (adj. p-value < 0.05). The mitochondrial transcriptomic profile also changed with time: we found two downregulated genes in mice between 8 and 12 weeks old (Ckmt2 and Cox6a2) and five DE genes between 12 and 16 weeks of age (Mavs, Tomm40L, Mtfp1, Ckmt2 and Cox6a2). The KEGG pathway analysis showed significant enrichment in pathways related to the autoimmune response and cytosolic DNA sensing. Our results suggest an important involvement of the immunological response, mainly cytosolic nucleic acid sensing, and mitochondrial signalling in the early stages of diabetes and obesity.
Niclosamide, but not ivermectin, inhibits anoctamin 1 and 6 and attenuates inflammation of the respiratory tract
Authors: Ousingsawat Jiraporn , Centeio Raquel , Schreiber Rainer , Kunzelmann Karl 
Published: November 2023

AbstractInflammatory airway diseases like cystic fibrosis, asthma and COVID-19 are characterized by high levels of pulmonary cytokines. Two well-established antiparasitic drugs, niclosamide and ivermectin, are intensively discussed for the treatment of viral inflammatory airway infections. Here, we examined these repurposed drugs with respect to their anti-inflammatory effects in airways in vivo and in vitro. Niclosamide reduced mucus content, eosinophilic infiltration and cell death in asthmatic mouse lungs in vivo and inhibited release of interleukins in the two differentiated airway epithelial cell lines CFBE and BCi-NS1.1 in vitro. Cytokine release was also inhibited by the knockdown of the Ca2+-activated Cl− channel anoctamin 1 (ANO1, TMEM16A) and the phospholipid scramblase anoctamin 6 (ANO6, TMEM16F), which have previously been shown to affect intracellular Ca2+ levels near the plasma membrane and to facilitate exocytosis. At concentrations around 200 nM, niclosamide inhibited inflammation, lowered intracellular Ca2+, acidified cytosolic pH and blocked activation of ANO1 and ANO6. It is suggested that niclosamide brings about its anti-inflammatory effects at least in part by inhibiting ANO1 and ANO6, and by lowering intracellular Ca2+ levels. In contrast to niclosamide, 1 µM ivermectin did not exert any of the effects described for niclosamide. The present data suggest niclosamide as an effective anti-inflammatory treatment in CF, asthma, and COVID-19, in addition to its previously reported antiviral effects. It has an advantageous concentration–response relationship and is known to be well tolerated.
Clinicopathological differences in focal segmental glomerulosclerosis depending on the accompanying pathophysiological conditions in renal allografts
Authors: Taneda Sekiko , Honda Kazuho , Koike Junki , Ito Naoko , Ishida Hideki , Takagi Toshio , Nagashima Yoji 
Published: November 2023

AbstractPrimary focal segmental glomerulosclerosis (FSGS) is thought to be caused by circulating factors leading to podocytopathy, whereas segmental sclerotic lesions (FSGS lesions) have several causes. We studied the clinicopathological differences of FSGS-lesions in 258 cases of FSGS in renal allografts, depending on the following accompanying pathophysiology: recurrence of primary FSGS, calcineurin inhibitor (CNI)-induced arteriolopathy, antibody-mediated rejection (ABMR), and other conditions. All cases were categorized with the Columbia classification. Recurrent FSGS developed the earliest after transplantation and showed the highest percentage of the collapsing (COL) variant in which collapse of the glomerular capillaries with epithelial hypertrophy was apparent. FSGS accompanying CNI-induced arteriolopathy predominantly developed the not otherwise specified (NOS) variant, showing severe ultrastructural endothelial injury. On the contrary, approximately 7% of the cases showed the COL variant, presenting glomerular endothelial damage such as double contours of glomerular basement membrane and endothelial cell swelling as well as epithelial cell proliferation. FSGS with ABMR had the highest creatinine levels and cellular variant percentage, with marked inflammation and ultrastructural endothelial injury. Approximately two-thirds of the cases without ABMR, CNI-induced arteriopathy, or recurrent FSGS had other coexisting conditions such as glomerulonephritis, T cell-mediated rejection, and reflux nephropathy with progressive tubulointerstitial fibrosis. Most of these cases were of the NOS variant. The clinicopathologic features of post-transplant FSGS differed depending on the associated conditions, and endothelial injury was apparent especially in cases of CNI-induced arteriolopathy and ABMR. Precise observation of FSGS lesions may facilitate the diagnosis and clinical management of FSGS during renal transplantation.
Worldwide disparities in access to treatment and investigations for nephropathic cystinosis: a 2023 perspective
Authors: Regnier Maitena , Flammier Sacha , Boutaba Mounia , Ndongo Aliou Abdoulaye , Servais Aude , Schaefer Franz , Levtchenko Elena , Bacchetta Justine , Bertholet-Thomas Aurélia 
Published: November 2023

Abstract
Background
Nephropathic cystinosis (NC) is a rare lysosomal disease, leading to early kidney failure and extra-renal comorbidities. Its prognosis strongly relies on early diagnosis and treatment by cysteamine. Developing economies (DEing) face many challenges when treating patients for rare and chronic diseases. The aim here is to evaluate the access to investigations and treatment in DEing, and to assess for potential inequalities with Developed Economies (DEed).

Methods
In this international cross-sectional study, a questionnaire on access, price and reimbursement of genetic, biological analyses, and treatment was sent to nephrology centers worldwide during 2022.

Results
A total of 109 centers responded, coming from 49 countries and managing 741 patients: 43 centers from 30 DEing and Economies in transition (TrE), and 66 from 19 DEed. In 2022, genetics availability was 63% in DEing and 100% in DEed, whereas intra leukocytes cystine levels (IL-CL) were available for 30% of DEing patients, and 94% of DEed patients, both increasing over the last decade, as has access to immediate release cysteamine and to cysteamine eye drops in DEing. However, delayed released cysteamine can be delivered to only 7% vs. 74% of patients from DEing and DEed, respectively, and is still poorly reimbursed in DEing.

Conclusions
Over the last decade, access to investigations (namely genetics and IL-CL) and to cysteamine have improved in DEing and TrE. However, discrepancies remain with DEed: access to delayed released cysteamine is limited, and reimbursement is still profoundly insufficient, therefore limiting their current use.

Graphical abstract
Adsorption of some cationic dyes onto two models of graphene oxide
Authors: Mounra Emma , Malloum Alhadji , Fifen Jean Jules , Conradie Jeanet 
Published: November 2023

Abstract

Context:

The search for highly efficient adsorbent materials remains a significant requirement in the field of adsorption for wastewater treatment. Computational study can highly contribute to the identification of efficient material. In this work, we propose a computational approach to study the adsorption of four cationic basic dyes, basic blue 26 (BB26), basic green 1 (BG1), basic yellow 2 (BY2), and basic red 1 (BR1), onto two models of graphene oxide as adsorbents. The main objectives of this study are the assessment of the adsorption capacity of the graphene oxide towards basic dyes and the evaluation of the environmental and temperature effects on the adsorption capacity. Quantum theory of atoms in molecules (QTAIM) analysis has been used to understand the interactions between the dyes and graphene oxides. In addition, adsorption free energies of the dyes onto graphene oxides are calculated in gas and solvent phases for temperatures varying from 200 to 400 K. As a result, the adsorption free energy varies linearly depending on the temperature, highlighting the importance of temperature effects in the adsorption processes. Furthermore, the results indicate that the environment (through the solvation) considerably affects the calculated adsorption free energies. Overall, the results show that the two models of graphene oxide used in this work are efficient for removing dyes from wastewater.

Methods:

We have optimized the complexes formed by the interaction of dyes with graphene oxides at the PW6B95-D3/def2-SVP level of theory. The SMD solvation model realizes the implicit solvation, and water is used as the solvent. Calculations are performed using the Gaussian 16 suite of program. QTAIM analysis is performed using the AIMAll program. Gibbs free energies as function of temperature are calculated using the TEMPO program.
“Listen to us”: small-scale farmers’ understandings of social-ecological changes and their drivers in Important Agricultural Heritage Systems
Authors: Caviedes Julián , Ibarra José Tomás , Calvet-Mir Laura , Junqueira André Braga 
Published: November 2023

AbstractCurrent social-ecological changes affect territories and people’s livelihoods worldwide. Many of these changes have detrimental effects on small-scale agricultural systems, with concomitant negative consequences on global and local food security and sovereignty. The objectives of this study were to explore (i) local knowledge on social-ecological changes and (ii) the perceived drivers of those changes occurring in a mountainscape and an islandscape in two Important Agricultural Heritage Systems of southern South America, both located within a Global Biodiversity Hotspot. This was done by conducting in-depth semi-structured interviews with local campesinos, whose livelihoods are based on the use and management of agrosilvopastoral systems. We found that local communities experience a wide range of globally and locally induced social-ecological changes acting in their territories. Campesinos mentioned 79 different observations of social-ecological changes and identified drivers for 77% of them. Changes in the atmospheric system, specifically regarding changes in precipitation, drought, and temperatures, were commonly observed by campesinos in both sites. Participants also observed complex interrelations between these changes and the drivers influencing them, climatic drivers being the most important. Even though general changes in climatic patterns were identified as drivers of changes by campesinos, other situated changes derived from the site’s biophysical, social, and economic conditions were also important. Our results highlight the importance of considering local knowledge to understand social-ecological changes and to support the development and implementation of public policies that promote contextualized adaptation measures to global changes that affect local livelihoods.
Clinical and imaging features of lymphomatosis cerebri: analysis of 8 cases and systematic review of the literature
Authors: Fan Mengke , Zhao Lu , Chen Qingjiang , Zhang Mingzhi , Zhang Xudong , Yang Zhihao , Li Suxiao , Song Yunfei 
Published: November 2023

AbstractLymphomatosis cerebri (LC) is a rare type of primary central nervous system lymphoma with diffuse, nonenhancing infiltrative lesions and is often misdiagnosed. Our study aimed to investigate the clinical characteristics and prognosis of LC through analyzing patients from the literature and our own center, so as to improve early diagnosis and treatment. PubMed, Web of Science and our hospital databases were reviewed, and information on demographic, clinical, pathological, cerebrospinal fluid (CSF), neuroimaging and treatment options was extracted. Univariate survival analysis was conducted by generating survival curves and comparing them using the log-rank test. Multivariate analysis was performed using the Cox proportional hazards regression model to identify the prognostic predictors. A total of 81 patients (median age: 58 years; interquartile range, IQR: 50–66.5 years), 45 males and 36 females, were included. The most common symptoms were cognitive impairment (65.4%) and gait impairment (50.6%). Imaging studies indicated that all 81 patients had supratentorial structure involvement, and 93.8% (76/81) had bilateral hemisphere involvement. There were 53.3% (32/60) patients with CSF pleocytosis and 65% (39/60) patients with increased CSF protein levels. The median time of diagnosis was 4.8 months (IQR: 2.3–6.9 months). Compared with 4 (95% CI: 1.78–6.22) months for all 81 patients, the median OS was 20 (95% CI: 8.24–31.76) months for those who had chemotherapy plus radiotherapy. Multivariate Cox analysis revealed that chemoradiotherapy (HR: 0.12; 95% CI: 0.02–0.68) and higher CSF glucose level (HR: 0.01; 95% CI: 0.00–0.26) were inversely associated with death. The diagnosis of LC should be alerted when neuroimaging with bilateral hemispheric involvement and CSF abnormality with pleocytosis and increased protein. Once the diagnosis is confirmed, the combination of chemotherapy and radiotherapy can be considered if the patient’s physical condition permits.Journal standard instruction requires an unstructured abstract. Kindly check and confirm.We have checked and confirmed that there is no problem.
Convolutional neural networks for accurate identification of mining remains from UAV-derived images
Authors: Fernández-Alonso Daniel , Fernández-Lozano Javier , García-Ordás María Teresa 
Published: November 2023

AbstractA new deep learning system is proposed for the rapid and accurate identification of anthropogenic elements of the Roman mining infrastructure in NW Iberia, providing a new approach for automatic recognition of different mining elements without the need for human intervention or implicit subjectivity. The recognition of archaeological and other abandoned mining elements provides an optimal test case for decision-making and management in a broad variety of research fields. A new image dataset was created by obtaining UAV images from different anthropic features. A convolutional neural network architecture was implemented, achieving recognition results of close to 95% accuracy. This methodological approach is suitable for the identification and accurate location of ancient mines and hydrologic infrastructure, providing new tools for accurate mapping of mining landforms. Additionally, this novel application of deep learning can be implemented to reduce potential risks caused by abandoned mines, which can cause significant annual human and economic losses worldwide.
Be Well™ Acres Homes: a community-driven, evidence-based approach to reduce health inequities through sustained cross-sector partnership
Authors: Rechis Ruth , Oestman Katherine B. , Walsh Michael T. , Love Brad , Hawk Ernest 
Published: November 2023

Abstract
Purpose
Be Well Communities™ is MD Anderson’s signature place-based approach for cancer prevention and control, working with communities to promote wellness and address modifiable risk factors for cancer. The purpose of this paper is to describe implementation of the planning phase of the Be Well Communities model in Acres Homes which began in 2019.

Methods
A community advisory group (Steering Committee) including residents, non-profit organizations, health care partners, city and county agencies, plus other stakeholders, was convened and aligned through a structured process to develop shared goals, foster multisector collaboration, as measured by a stakeholder survey administered twice, and enhance community capacity to improve health outcomes through development of a Community Action Plan.

Results
Clear, achievable goals were developed, multisector collaboration was enhanced, and more than 400 h of capacity building support led to a Community Action Plan initially focused on healthy eating and active living, including 15 evidence-based interventions led by 18 organizations. The majority (93%) of the Steering Committee reports that this plan reflects community priorities and will reach the residents most in need.

Conclusion
By listening and developing trust, the Be Well Communities team successfully worked with Acres Homes residents and organizations to enhance community capacity to address health inequities in one of Houston’s most diverse and historic communities.
Navigating the metric maze: a taxonomy of evaluation metrics for anomaly detection in time series
Authors: Sørbø Sondre , Ruocco Massimiliano 
Published: November 2023

AbstractThe field of time series anomaly detection is constantly advancing, with several methods available, making it a challenge to determine the most appropriate method for a specific domain. The evaluation of these methods is facilitated by the use of metrics, which vary widely in their properties. Despite the existence of new evaluation metrics, there is limited agreement on which metrics are best suited for specific scenarios and domains, and the most commonly used metrics have faced criticism in the literature. This paper provides a comprehensive overview of the metrics used for the evaluation of time series anomaly detection methods, and also defines a taxonomy of these based on how they are calculated. By defining a set of properties for evaluation metrics and a set of specific case studies and experiments, twenty metrics are analyzed and discussed in detail, highlighting the unique suitability of each for specific tasks. Through extensive experimentation and analysis, this paper argues that the choice of evaluation metric must be made with care, taking into account the specific requirements of the task at hand.
Fast Kötter–Nielsen–Høholdt interpolation over skew polynomial rings and its application in coding theory
Authors: Bartz Hannes , Jerkovits Thomas , Rosenkilde Johan 
Published: November 2023

AbstractSkew polynomials are a class of non-commutative polynomials that have several applications in computer science, coding theory and cryptography. In particular, skew polynomials can be used to construct and decode evaluation codes in several metrics, like e.g. the Hamming, rank, sum-rank and skew metric. We propose a fast divide-and-conquer variant of Kötter–Nielsen–Høholdt (KNH) interpolation algorithm: it inputs a list of linear functionals on skew polynomial vectors, and outputs a reduced Gröbner basis of their kernel intersection. We show, that the proposed KNH interpolation can be used to solve the interpolation step of interpolation-based decoding of interleaved Gabidulin codes in the rank-metric, linearized Reed–Solomon codes in the sum-rank metric and skew Reed–Solomon codes in the skew metric requiring at most $${\widetilde{O}}\left( s^\omega {\mathfrak {M}}(n)\right) $$

O
~

s
ω

M

(
n
)

operations in $${\mathbb {F}}_{q^m}$$

F

q
m

, where n is the length of the code, $$s$$
s
the interleaving order, $${\mathfrak {M}}(n)$$

M
(
n
)

the complexity for multiplying two skew polynomials of degree at most n, $$\omega $$
ω
the matrix multiplication exponent and $${\widetilde{O}}\left( \cdot \right) $$

O
~

·

the soft-O notation which neglects log factors. This matches the previous best speeds for these tasks, which were obtained by top–down minimal approximant bases techniques, and complements the theory of efficient interpolation over free skew polynomial modules by the bottom-up KNH approach. In contrast to the top–down approach the bottom-up KNH algorithm has no requirements on the interpolation points and thus does not require any pre-processing.