bluuebunny/crossref_metadata_2025 huggingface dataset:
Cultivation and molecular characterization of viable Helicobacter pylori from the root canal of 170 deciduous teeth of children
Authors: Elger Wieland , Tegtmeyer Nicole , Rohde Manfred , Linz Bodo , Hirsch Christian , Backert Steffen
Published: December 2024

Background

Helicobacter pylori is a persistent pathogen in the human stomach. However, the proposed transmission route via the oral cavity is not understood and under intense debate. While dozens of studies have shown by PCR that H. pylori DNA is frequently present in the oral cavity, data on the growth and characterization of viable H. pylori from this compartment are very scarce, and it is unclear whether the bacteria can survive in the oral cavity for longer time periods or even colonize it.

Methods

Selective growth methods, scanning electron microscopy, urease assay, Western blotting, PCR, and gene sequencing were applied to identify and examine viable H. pylori in decayed milk teeth.

Results

Here, we studied viable H. pylori in the plaque and root canals of 170 endodontically infected deciduous teeth that were extracted from 54 children. While H. pylori DNA was detected in several plaque and many root canal samples by PCR, live bacteria could only be cultivated from 28 root canals, but not from plaque. These 28 isolates have been identified as H. pylori by PCR and sequencing of vacA, cagA and htrA genes, phylogenetic analyses, protein expression of major H. pylori virulence factors, and by signal transduction events during infection of human cell lines.

Conclusions

Thus, the microaerobic environment in the root canals of endodontically infected teeth may represent a protected and transient reservoir for live H. pylori, especially in individuals with poor dental hygiene, which could serve as a potential source for re-infection of the stomach after antibiotic therapy or for transmission to other individuals.
Receptor tyrosine kinase inhibition leads to regression of acral melanoma by targeting the tumor microenvironment
Authors: Smith Eric A. , Belote Rachel L. , Cruz Nelly M. , Moustafa Tarek E. , Becker Carly A. , Jiang Amanda , Alizada Shukran , Prokofyeva Anastasia , Chan Tsz Yin , Seasor Tori A. , Balatico Michael , Cortes-Sanchez Emilio , Lum David H. , Hyngstrom John R. , Zeng Hanlin , Deacon Dekker C. , Grossmann Allie H. , White Richard M. , Zangle Thomas A. , Judson-Torres Robert L.
Published: December 2024

Background

Acral melanoma (AM) is an aggressive melanoma variant that arises from palmar, plantar, and nail unit melanocytes. Compared to non-acral cutaneous melanoma (CM), AM is biologically distinct, has an equal incidence across genetic ancestries, typically presents in advanced stage disease, is less responsive to therapy, and has an overall worse prognosis.

Methods

An independent analysis of published sequencing data was performed to evaluate the frequency of receptor tyrosine kinase (RTK) ligands and adapter protein gene variants and expression. To target these genetic variants, a zebrafish acral melanoma model and preclinical patient-derived xenograft (PDX) mouse models were treated with a panel of RTK inhibitors. Residual PDX tumors were evaluated for changes in proliferation, vasculature, necrosis, and ferroptosis by histology and immunohistochemistry.

Results

RTK ligands and adapter proteins are frequently amplified, translocated, and/or overexpressed in AM. Dual FGFR/VEGFR inhibitors decrease acral-analogous melanocyte proliferation and migration in zebrafish, and the potent pan-FGFR/VEGFR inhibitor, Lenvatinib, uniformly induces tumor regression in AM PDX tumors but only slows tumor growth in CM models. Unlike other multi-RTK inhibitors, Lenvatinib is not directly cytotoxic to dissociated AM PDX tumor cells and instead disrupts tumor architecture and vascular networks.

Conclusion

Considering the great difficulty in establishing AM cell culture lines, these findings suggest that AM may be more sensitive to microenvironment perturbations than CM. In conclusion, dual FGFR/VEGFR inhibition may be a viable therapeutic strategy that targets the unique biology of AM.
Efficacy of colistin-based combinations against pandrug-resistant whole-genome-sequenced Klebsiella pneumoniae isolated from hospitalized patients in Egypt: an in vitro/vivo comparative study
Authors: Attalla Eriny T. , Khalil Amal M. , Zakaria Azza S. , Evans Rhiannon , Tolba Nesrin S. , Mohamed Nelly M.
Published: December 2024

Background

Colistin resistance significantly constrains available treatment options and results in the emergence of pandrug-resistant (PDR) strains. Treating PDR infections is a major public health issue. A promising solution lies in using colistin-based combinations. Despite the availability of in vitro data evaluating these combinations, the in vivo studies remain limited.

Results

Thirty colistin-resistant Klebsiella pneumoniae (ColRKp) isolates were collected from hospitalized patients. Colistin resistance was detected using broth microdilution, and antimicrobial susceptibility was tested using the Kirby-Bauer method against 18 antibiotics. Extremely high resistance levels were detected, with 17% of the isolates being PDR. Virulence profiling, assessed using Anthony capsule staining, the string test, and the crystal violet assay, indicated the predominance of non-biofilm formers and non-hypermucoid strains. The isolates were screened for mcr genes using polymerase chain reaction. Whole-genome sequencing (WGS) and bioinformatics analysis were performed to characterize the genomes of PDR isolates. No plasmid-borne mcr genes were detected, and WGS analysis revealed that PDR isolates belonged to the high-risk clones: ST14 (n = 1), ST147 (n = 2), and ST383 (n = 2). They carried genes encoding extended-spectrum β-lactamases and carbapenemases, blaCTX-M-15 and blaNDM-5, on conjugative IncHI1B/IncFIB plasmids, illustrating the convergence of virulence and resistance genes. The most common mechanism of colistin resistance involved alterations in mgrB. Furthermore, deleterious amino acid substitutions were also detected within PhoQ, PmrC, CrrB, ArnB, and ArnT. Seven colistin-containing combinations were compared using the checkerboard experiment. Synergy was observed when combining colistin with tigecycline, doxycycline, levofloxacin, ciprofloxacin, sulfamethoxazole/trimethoprim, imipenem, or meropenem. The efficacy of colistin combined with either doxycycline or levofloxacin was assessed in vitro using a resistance modulation assay, and in vivo, using a murine infection model. In vitro, doxycycline and levofloxacin reversed colistin resistance in 80% and 73.3% of the population, respectively. In vivo, the colistin + doxycycline combination demonstrated superiority over colistin + levofloxacin, rescuing 80% of infected animals, and reducing bacterial bioburden in the liver and kidneys while preserving nearly intact lung histology.

Conclusions

This study represents the first comparative in vitro and in vivo investigation of the efficacy of colistin + doxycycline and colistin + levofloxacin combinations in clinical PDR ColRKp isolates characterized at a genomic level.
Wildfire assessment using machine learning algorithms in different regions
Authors: Moghim Sanaz , Mehrabi Majid
Published: December 2024

Background

Climate change and human activities are two main forces that affect the intensity, duration, and frequency of wildfires, which can lead to risks and hazards to the ecosystems. This study uses machine learning (ML) as an effective tool for predicting wildfires using historical data and influential variables. The performance of two machine learning algorithms, including logistic regression (LR) and random forest (RF), to construct wildfire susceptibility maps is evaluated in regions with different physical features (Okanogan region in the US and Jamésie region in Canada). The models’ inputs are eleven physically related variables to output wildfire probabilities.

Results

Results indicate that the most important variables in both areas are land cover, temperature, wind, elevation, precipitation, and normalized vegetation difference index. In addition, results reveal that both models have temporal and spatial generalization capability to predict annual wildfire probability at different times and locations. Generally, the RF outperforms the LR model in almost all cases. The outputs of the models provide wildfire susceptibility maps with different levels of severity (from very high to very low). Results highlight the areas that are more vulnerable to fire. The developed models and analysis are valuable for emergency planners and decision-makers in identifying critical regions and implementing preventive action for ecological conservation.
Psychosis associated with cannabis withdrawal: systematic review and case series
Authors: Chesney Edward , Reilly Thomas J. , Scott Fraser , Slimani Ikram , Sarma Ananya , Kornblum Daisy , Oliver Dominic , McGuire Philip
Published: December 2024

Background

Abrupt cessation of heavy cannabis use can cause a withdrawal syndrome characterised by irritability, anxiety, insomnia, reduced appetite and restlessness. Recent reports have also described people in whom cannabis withdrawal immediately preceded the acute onset of psychosis.

Aims

To identify cases of psychosis associated with cannabis withdrawal.

Method

We completed a systematic review of the literature, which comprised case reports, case series and other studies. We also searched a large electronic database of psychiatric healthcare records.

Results

The systematic review identified 44 individuals from 21 studies in whom cannabis withdrawal preceded the development of acute psychosis. In the health record study, we identified another 68 people, of whom 47 involved a first episode of psychosis and 21 represented further episodes of an existing psychotic disorder. Almost all people were daily cannabis users who had stopped using cannabis abruptly. Individuals who continued to use cannabis after the acute psychotic episode had a much higher risk of subsequent relapse than those who abstained (odds ratio 13.9 [95% CI: 4.1 to 56.9]; χ2 = 20.1, P < 0.00001).

Conclusions

Abrupt cannabis withdrawal may act as a trigger for the first episode of psychosis and a relapse of an existing psychosis. Acute psychotic symptoms can emerge after the cessation, as well as following the use, of cannabis.
Give Patients the Choice to Test for DPD Deficiency Before Fluoropyrimidine Chemotherapy
Authors: Surprenant Ken , Murray Lindsay , Merritt Karen , Hopkins Maria , McIntyre Joanne
Published: December 2024

Patients, not physicians, should decide if DPYD screening is right for them before FU/Xeloda chemotherapy.
Nectin-4 Positivity in Genitourinary Malignancies: A Systematic Review
Authors: Crupi Emanuele , Costa de Padua Tiago , Marandino Laura , Fallara Giuseppe , Pederzoli Filippo , Cimadamore Alessia , Goetz Emanuele C. , Cigliola Antonio , Patané Damiano A. , Mercinelli Chiara , Tateo Valentina , Salonia Andrea , Briganti Alberto , Montorsi Francesco , Meeks Joshua J. , Spiess Philippe E. , Alhalabi Omar , Gao Jianjun , Kamat Ashish M. , Grivas Petros , Necchi Andrea , Raggi Daniele
Published: December 2024

PURPOSE

Aberrant expression of nectin-4 (N4) has been observed in several malignancies emerging as new target for antibody-drug conjugates, especially in urothelial carcinoma of the bladder (UBC). Limited data on N4 positivity in nonurothelial genitourinary (GU) cancers are available. This systematic-review aimed to investigate N4 positivity among GU malignancies.

METHODS

A systematic literature review was performed on March 2023 using PubMed, MEDLINE, and Embase databases according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Protocol was amended to incorporate a new updated search on March 2024.

RESULTS

Twenty-five studies evaluating N4 positivity in GU tumors were included, 14 on UBC, three on upper tract urothelial carcinoma (UTUC), six on histologic subtypes (HS) and divergent histology of the bladder, one on papillary renal cell carcinoma (pRCC), one in chromophobe RCC (chRCC), two on penile cancer, one in prostate cancer (PCa). Among UBC, stratifying per stage N4 positivity was higher in metastatic (weighted mean [WM], 90.8; range, 59.6-100) and in non–muscle-invasive (WM, 87.4; range, 86.7-88.3) than in muscle-invasive UC (WM, 83.1; range, 68.2-100). The N4 positivity of UBC was higher than UTUC (WM, 62.9; range, 44.4-65.7). Immunohistochemistry N4 positivity was reported to be lower in non-UC malignancies, including pRCC (WM, 44.1; range, 44.1-44.1), HS (WM, 63.5; range, 0-100), PCa (WM0; range, 0-0), chRCC (WM, 18.5; range, 18.5-18.5), and penile cancer (WM, 86.5; range, 61.4-98.3), compared with UBC overall (WM, 87.1; range, 59.6-100).

CONCLUSION

Non-UC malignancies seem to have a lower N4 positivity rate than UC. N4 positivity in bladder cancer appears to vary according to stage and presence of HS. The predictive and prognostic role of N4 must be further characterized in larger and prospective studies.
CompLex: Legal systems through the lens of complexity science
Authors: Vivo Pierpaolo , Katz Daniel M. , Ruhl J. B.
Published: December 2024

While “complexity science” has achieved significant successes in several interdisciplinary fields such as economics and biology, it is only a very recent observation that legal systems —from the way legal texts are drafted and connected to the rest of the corpus, up to the level of how judges and courts reach decisions under a variety of conflicting inputs— share several features with standard Complex Adaptive Systems. This review is meant as a gentle introduction to the use of quantitative tools and techniques of complexity science to describe, analyse, and tame the complex web of human interactions that the Law is supposed to regulate. We offer an overview of the main directions of research undertaken so far as well as an outlook for future research, and we argue that statistical physicists and complexity scientists should not ignore the opportunities offered by the cross-fertilisation between legal scholarship and complex-systems modelling.
Maternal Migration and Child Fostering Arrangements in Nairobi's Slums
Authors: Cotton Cassandra , Oduor Clement
Published: December 2024

Child fostering—children living apart from their biological mothers—is an established strategy to support children and families throughout Africa. Little is known about how fostering decisions might be influenced by maternal migration and place of residence when women move to urban slums, which are home to a sizable proportion of Africa's urban population. Using a mixed-methods approach, we triangulate in-depth interviews with birth histories collected in two slum settlements in Nairobi, Kenya, to explore the interconnections between maternal migration experience, slum residence, and child fostering decisions. Our quantitative results reveal substantial fostering of children among women in slum contexts, with fostering being significantly higher among children of migrant women, particularly those who have recently arrived. Qualitative findings suggest that migration acts as an important impetus to foster, as do transitions in women's romantic relationships, economic uncertainty, poor slum conditions, and desires to send children to rural areas for schooling. This novel finding on children's schooling is supported in quantitative analyses, which show that older school-age children are more likely than younger children to be fostered. This study highlights the central roles of maternal migration, economic and social precariousness, and place of residence in determining the fostering of children among mothers living in informal settlements.
Under Pressure
Authors: Brzezinski Max
Published: December 2024

In 1981, David Bowie and Queen both happened to be in Switzerland: They met and made “Under Pressure.” Recorded on a lark, the song broke the path for subsequent pop anthems. In Under Pressure, Max Brzezinski tells the classic track’s story, charting the relationship between pop music, collective politics, and dominant institutions of state, corporations, and civil society. Brzezinski shows that, like all great pop anthems, “Under Pressure” harnesses collective sentiments in order to model new ways of thinking and acting. As we continue to live under the sign of the global oppressive power the song names, analyzes, and attempts to move beyond, we remain, in Bowie and Freddie Mercury’s phrase, under pressure.
Hemodynamic Assessment Using SPY Laser Fluorescence Imaging During Pancreatoduodenectomy with Common Hepatic Artery Resection
Authors: Fuji Tomokazu , Takagi Kosei , Yasui Kazuya , Nishiyama Takeyoshi , Yamada Motohiko , Nagai Yasuo , Kanehira Noriyuki , Fujiwara Toshiyoshi
Published: December 2024

Background

Pancreatectomies combined with arterial resection can be indicated for pancreatic cancer. In a pancreatectomy with arterial resection, intraoperative confirmation of blood flow through reconstructed vessels is crucial. This study highlights the usefulness of SPY laser fluorescence imaging during a pancreatoduodenectomy with common hepatic artery resection (PD-CHAR).

Patient and Methods

A 55-year-old man with borderline resectable pancreatic head cancer underwent a PD-CHAR. After confirming tumor resectability, reconstruction of the CHA to the proper hepatic artery was performed. Subsequently, the superior mesenteric vein was reconstructed.

Results

SPY laser fluorescence imaging demonstrated arterial blood perfusion to the liver through the reconstructed hepatic artery, followed by perfusion from the portal vein. The operation lasted 493 min, with an estimated blood loss of 400 mL. The postoperative course was uneventful with good arterial blood flow.

Conclusion

The SPY Portable Handheld Imager could be valuable for visualizing blood flow in reconstructed vessels and assessing tissue perfusion during a pancreatectomy combined with vascular reconstruction.
Improved precision, sensitivity, and adaptability of ordered two-template relay cDNA library preparation for RNA sequencing
Authors: Ferguson Lucas , Upton Heather E. , Pimentel Sydney C. , Jeans Chris , Ingolia Nicholas T. , Collins Kathleen
Published: December 2024

Sequencing RNAs that are biologically processed or degraded to less than ∼100 nt typically involves multistep, low-yield protocols with bias and information loss inherent to ligation and/or polynucleotide tailing. We recently introduced ordered two-template relay (OTTR), a method that captures obligatorily end-to-end sequences of input molecules and, in the same reverse transcription step, also appends 5′ and 3′ sequencing adapters of choice. OTTR has been thoroughly benchmarked for optimal production of microRNA, tRNA and tRNA fragments, and ribosome-protected mRNA footprint libraries. Here we sought to characterize, quantify, and ameliorate any remaining bias or imprecision in the end-to-end capture of RNA sequences. We introduce new metrics for the evaluation of sequence capture and use them to optimize reaction buffers, reverse transcriptase sequence, adapter oligonucleotides, and overall workflow. Modifications of the reverse transcriptase and adapter oligonucleotides increased the 3′ and 5′ end-precision of sequence capture and minimized overall library bias. Improvements in recombinant expression and purification of the truncatedBombyx moriR2 reverse transcriptase used in OTTR reduced nonproductive sequencing reads by minimizing bacterial nucleic acids that compete with low-input RNA molecules for cDNA synthesis, such that with miRNA input of 3 pg (<1 fmol), fewer than 10% of sequencing reads are bacterial nucleic acid contaminants. We also introduce a rapid, automation-compatible OTTR protocol that enables gel-free, length-agnostic enrichment of cDNA duplexes from unwanted adapter-only side products. Overall, this work informs considerations for unbiased end-to-end capture and annotation of RNAs independent of their sequence, structure, or posttranscriptional modifications.
Δοκίμια φορολογικής επιβολής και συμμόρφωσης
Authors: Σκιαδοπούλου Σταυρούλα
Published: December 2024

Η παρούσα διατριβή ασχολείται με θέματα που αφορούν στην φοροαποφυγή των επιχειρήσεων στην Ελλάδα την περίοδο 2006-2014.. Η διερεύνηση των υποθέσεων υλοποιείται με τη χρήση μιας πλούσιας βάσης δεδομένων που προέκυψε από τη συνένωση τεσσάρων διαφορετικών πηγών. Αναφορικά με τη μεθοδολογία ακολουθούμε τη σύγχρονη βιβλιογραφία και βασιζόμαστε κυρίως στη μέθοδο διαφοράς των διαφορών (diff in diff) για να εξετάσουμε εάν ορισμένα γεγονότα (events) που οφείλονται σε κάποια ενέργεια της φορολογικής διοίκησης άμεση (π.χ. φορολογικός έλεγχος) ή έμμεση (έκδοση υπουργικών αποφάσεων, ανάπτυξη ηλεκτρονικών εφαρμογών, οργανωτικές αλλαγές του ελεγκτικού μηχανισμού) και αφορούν σε μια ομάδα επιχειρήσεων, επηρέασαν τη φοροαποφυγή των επιχειρήσεων αυτών σε σχέση με άλλη ομάδα επιχειρήσεων που δεν υπέστησαν αυτήν την ενέργεια (ουδέτερο δείγμα).
Optimizing processes of operational simulation in transport and dispersion of oil slicks and decision support and response systems
Authors: Κεραμέα Παναγιώτα
Published: December 2024

Ένα σημαντικό ζήτημα στον κόσμο που εξαρτάται από το πετρέλαιο είναι η τυχαία διαρροή του, η ρύπανση καθώς και οι αντίστοιχες τεράστιες περιβαλλοντικές επιπτώσεις. Ως εκ τούτου, είναι απαραίτητο να αντιμετωπιστεί αυτό το ζήτημα εφαρμόζοντας φιλικές προς το περιβάλλον μεθόδους. Πολλά αριθμητικά μοντέλα πετρελαιοκηλίδων χρησιμοποιούνται παγκοσμίως για την προσομοίωση της εξέλιξης μιας πετρελαιοκηλίδας. Η προσομοίωση της μεταφοράς και της διασποράς μιας πετρελαιοκηλίδας στη θάλασσα, αξιολογώντας τις φυσικοχημικές διεργασίες που λαμβάνουν χώρα μεταξύ της φάσης του πετρελαίου και της υδάτινης στήλης, είναι η βάση για τον εντοπισμό και την αξιολόγηση της περιβαλλοντικής της επίδρασης. Έτσι, αυτή η διδακτορική διατριβή στοχεύει στη βελτίωση της κατανόησής μας για τον αντίκτυπο των φυσικών διεργασιών (όπως η μεταφορά και η διασπορά της πετρελαιοκηλίδας) και εστιάζει στις διεργασίες πετρελαϊκής αποσύνθεσης (ιδιαίτερα στη βιοαποικοδόμηση), βελτιώνοντας την παραμετροποίησή της μέσω μιας σειράς εργαστηριακών πειραμάτων. Το μοντέλο πετρελαιοκηλίδας OpenDrift, σε συνδυασμό με μετεωρολογικά, υδροδυναμικά και κυματικά μοντέλα, χρησιμοποιήθηκε για αυτήν την ανάλυση. Η βελτιωμένη ρουτίνα βιοαποικοδόμησης τελικά ενσωματώθηκε στον αλγόριθμο OpenDrift, βελτιώνοντας τον μεσοπρόθεσμο έως μακροπρόθεσμο προϋπολογισμό πετρελαίου. Οι προσομοιώσεις της συμπεριφοράς της πετρελαιοκηλίδας πραγματοποιήθηκαν μέσω στατιστικά παραγόμενων συνόλων για τους ανέμους και τα επιφανειακά ρεύματα. Τα αποτελέσματα του μοντέλου αξιολογήθηκαν σε σχέση με παρατηρήσεις δορυφόρων χρησιμοποιώντας μια σειρά από μετρικές. Ο δείκτης εκτίμησης κινδύνου πετρελαιοκηλίδας και ο δείκτης τρωτότητας πετρελαιοκηλίδας χαρτογραφήθηκαν, ποσοτικοποιώντας τους κινδύνους και τις αβεβαιότητες στις προσομοιώσεις πετρελαιοκηλίδων. Σε όλες τις προσομοιώσεις, τα δεδομένα ανέμων σε πραγματικό χρόνο παρέχονταν από τα μοντέλα NOAA-GFS και ECMWF, τα υδροδυναμικά δεδομένα παρήχθησαν από το μοντέλο υψηλής ανάλυσης AEM 3D και ελήφθησαν από τα μοντέλα CMEMS (NEMO), HYCOM και CYCOFOS, και τα δεδομένα κυμάτων ελήφθησαν από το μοντέλο υψηλής ανάλυσης SWAN και τα μοντέλα CMEMS (WAM και WAVEWATCH-III). Τέλος, ο απώτερος στόχος αυτής της έρευνας ήταν η διάδοση και η επιχειρησιακή χρήση των παραγόμενων αποτελεσμάτων σε τοπικούς φορείς, όπως οι Λιμενικές Αρχές της Καβάλας και της Αλεξανδρούπολης και η Energean Oil & Gas SA.
Factors Influencing Climate-Smart Agriculture Practices Adoption and Crop Productivity among Smallholder Farmers in Nyimba District, Zambia
Authors: Petros Chavula , Feyissa Samuel , Sileshi Million , Shepande Chizumba
Published: December 2024

Climate change significantly affects smallholder farmers, whose livelihoods are closely tied to the environment. This study explores factors influencing the adoption of climate-smart agriculture (CSA) practices and their impact on crop productivity among small-scale farmers in Nyimba District, Zambia. Data were collected from 194 households across 12 villages, and logistic regression and propensity score matching analyses were employed to identify key factors and evaluate CSA’s effects on crop yields. Findings revealed that CSA adoption is influenced by factors such as education level, household size, fertilizer use, age, gender, farming experience, livestock ownership, income, farmland size, marital status, and access to climate-related information. CSA adopters experienced a 20.20% increase in overall crop yields compared to non-adopters, with a 21.50% increase in maize yields specifically. The study underscores the need for targeted interventions to support CSA adoption through education, improved dissemination of climate information, and access to critical resources such as improved seeds and financial services. This research offers insights for policymakers and extension services to develop evidence-based strategies enhancing resilience and productivity among smallholder farmers in response to climate challenges.
Association of Triglyceride glucose index with the outcomes of Ischemic stroke.
Authors: Bibi Chaand , Khan Ahmad Hassan , Kashif Muhammad , Khan Maaz , Iftikhar Syed Muhammad Shoaib
Published: December 2024

Background Ischemic stroke is a primary contributor to both mortality and disability on a global scale. The triglyceride-glucose index (TyG index), which measures insulin resistance, has been found as a possible predictor of outcomes of cerebrovascular events. Objective To examine the correlation between TyG index and outcomes in patients diagnosed with ischemic stroke. Methods This retrospective analysis of 200 patients diagnosed with ischemic stroke was carried out at the department of medicine, Khyber Teaching Hospital, Peshawar between 1st August 2022 and 31st December 2023. Triglyceride/glucose ratio was determined using the formula TyG = ln [Fasting triglycerides (mg/dl)/Fasting glucose (mg/dl)]/2. Patients were categorized into two Group A (TyG index < 8.8) and Group B (TyG index > 8.8). Demographic data, clinical features, and stroke outcomes, such as death and functional status (assessed by the modified Rankin Scale [mRS]), were compared between the two groups. Results Group A contained (112) patients and Group B (88). Both Group A and Group B had 51.8% (n=58) and 51.1% (n=45) male patients respectively. The mean age of patients in Group A was 65.4 ± 10.2 years and 67.1 ± 11.5 years in group B. 30-day mortality in group A was 8.0% (n=9) and 18.2% (n=16) in group B (p value 0.03). The median mRS score at 3 months in group A was 2.5 versus 3.5 in group B (p value = 0.02). Patients in Group B had longer hospital stay (10.5 ± 3.1days vs. 8.2 ± 2.4days, p = 0.01) and higher frequency of major adverse cardiovascular events (MACE) (15% vs. 7%, p = 0.05). Conclusion In ischemic stroke patients, 30-day mortality was more common with TyG index >8.8 and the modified Rankin Scale (mRS) functional status at 3 months was better in TyG index <8.8.
Internowana czyli pamiętnik podwójnie pisany
Authors: Sierotwińska-Rewicka Muzia , Rewicka Berenika
Published: December 2024

Seria Pokolenie „Solidarności” powstała w celu przedstawienia Czytelnikom relacji uczestników wydarzeń związanych z dziejami opozycji antykomunistycznej w PRL-u, szczególnie związku zawodowego NSZZ „Solidarność”, który władza totalitarnego państwa próbowała zniszczyć, wprowadzając 13 grudnia 1981 roku stan wojenny. Autorzy, świadkowie dziejów pierwszych lat „Solidarności” i stanu wojennego, swoje przeżycia spisali w różnych formach literackich: listach, wspomnieniach, poematach, pamiętnikach, dramatach. Edycja tych tekstów nie polegała na ich opracowaniu literackim – zweryfikowano jedynie fakty historyczne zawarte w książce i objaśniono znaczenie niektórych słów oraz przybliżono wydarzenia, które mogą być niejasne dla współczesnego Czytelnika. Pozostawiono teksty w ich autentycznej formie, ograniczając redaktorską ingerencję do uwspółcześnienia interpunkcji, poprawy ortografii i gramatyki oraz wyjaśnienia niezrozumiałych miejsc. Każdy tom zawiera krótkie biografie autorów oraz indeks osób. Niniejsza publikacja to „dwugłos” Marii Sierotwińskiej-Rewickiej i Bereniki Rewickiej, wspomnienia pisane na przemian z punktu widzenia matki i córki.
A Polyhedral Study of Multivariate Decision Trees
Authors: Michini Carla , Zhou Zachary
Published: December 2024

Decision trees are a widely used tool for interpretable machine learning. Multivariate decision trees employ hyperplanes at the branch nodes to route datapoints throughout the tree and yield more compact models than univariate trees. Recently, mixed-integer programming (MIP) has been applied to formulate the optimal decision tree problem. A key component of most MIP formulations is a specification of how to route datapoints in the tree from the root to the leaves. Our goal is to provide polyhedral characterizations of realizable routings, that is, routings that can be realized using multivariate branching rules. We first focus on shattering inequalities, a class of valid inequalities that can be used to strengthen almost any MIP formulation and that have been shown to be computationally effective. We prove that if all the feature vectors are in general position, then the shattering inequalities defined for the root of the tree are facet defining for the convex hull of the realizable routings. We then show that every facet-defining inequality of a depth one tree involving at least two variables is also facet defining for trees of arbitrary depth. Finally, we show that facet-defining inequalities characterizing realizable routings are also facet-defining for a complete MIP formulation. We validate our theoretical results by performing numerical experiments that specifically exploit shattering inequalities defined at the root node and we observe an improvement in performance for both numerical and categorical data sets, especially for decision trees of intermediate size.

Funding: C. Michini gratefully acknowledges funding from the DoD, Air Force [Award FA9550-23-1-0487].
Potential Effects of Clitoria ternatea on Rotenone-Induced Rat Model of Parkinson Disease
Authors:   Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Selangor, Malaysia, Umbar Genevieve Simboh Anak , Dayana Hani Qistina ,   Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Selangor, Malaysia, Muhammad Hussin ,   Toxicology & Pharmacology Unit, Herbal Medicine Research Center, Institute for Medical Research, National Institute of Health, Setia Alam Selangor, Malaysia, Ahad Mohamad Anuar ,   Department of Basic Health Sciences, Faculty of Pharmacy & Biomedical Sciences, MAHSA University, 42610 Jenjarom Selangor, Malaysia, Zulkapli Azlina ,   Laboratory Animal Resources Unit, Special Resource Center, Institute for Medical Research, National Institute of Health, Malaysia, Eshak Zolkapli ,   Department of Pharmacology and Chemistry, Faculty of Pharmacy, UiTM Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Che Ramli Muhammad Danial ,   Department of Diagnostic and Allied Health Sciences, Faculty of Health and Life Sciences, Management and Science University, 40100 Shah Alam, Selangor, Malaysia
Published: December 2024

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterised by motor dysfunction due to the loss of dopaminergic neurons in the substantia nigra. Clitoria ternatea (CT), a medicinal plant used in Ayurvedic medicine, has shown promising neuroprotective properties that may be beneficial in the context of PD. This study investigates the potential effects of CT on a rotenone-induced rat model of Parkinson's disease. Sixty adult male Sprague Dawley rats were divided into six groups: the normal control group, the positive control group treated with Levodopa, the negative control group, and three experimental groups treated with CT extract at doses of 150 mg/kg, 250 mg/kg, and 500 mg/kg, respectively, for 28 days. Behavioural analyses, including motor and cognitive assessments, and histological examinations were performed. The group treated with the highest dose (500 mg/kg) showed the most significant reduction in immobility time from day 1 to day 28. Anxiety-like behaviour was assessed using the open field test, and motor impairment was evaluated with the beam walking test. The highest dose group showed a significant increase in total distance travelled, from 72.3% to 95.4% over the treatment period, compared to the control groups. Histological analysis revealed that the 500 mg/kg treatment group had the most substantial reduction in Lewy bodies. Overall, the administration of CT extract at 500 mg/kg improved motor deficits, neurobehavioral performance, and reduced neurodegeneration. These findings suggest that CT could be a promising natural therapeutic agent for the treatment and management of PD.
The Difficulty of Reality and the Difficulty of Criticism
Authors: Chaouli Michel
Published: December 2024

Abstract: There are two points I aim to make here. One is that an appeal to a common sphere is woven into the very act of criticism. Criticism becomes urgent the moment something in the world outpaces our capacities for coping. Such confrontations urge us to speak—to do something—about this difficulty. That is the wellspring of criticism: when faced with an experience that capsizes our systems of ordering the world, we seek to make sense of what surpasses sense, and we do so by turning to others. The second point is that the shape, boundary, and texture of this common is not available as something that can be known and described ahead of time. It emerges (if it emerges) in the act of criticism itself. It is not there before, and it need not endure. An act of criticism can forge commonality, solidarity, and purpose, but it can also (and for the same reasons) divide and frustrate. That is because in a real encounter with a significant work not-knowing is as primal as knowing. A third idea follows from the first two: real criticism does not lend itself to becoming a tool for political action, not because it is not political, but because it is not a tool.
Selection of robust metrics for the position and width of hyperspectral response functions via a simulation approach
Authors: Perry David , Conran David , Skauli Torbjorn
Published: December 2024

The IEEE P4001 hyperspectral camera standard and the need for
time-efficient response function test metrics are introduced.
Representative center and width metrics applicable to the
specification of spatial and spectral response functions are
presented. A simulation approach for determining trends in metric
behavior as a function of lab collection parameters is described.
Algorithm results are enumerated for a variety of hypothetical imager
response shapes and width categories under fixed accuracy
requirements. Metric flexibility, limiting sample rates, and lab test
time estimates are compared and recommendations are made for the P4001
standard. The centroid center metric and standard deviation width
algorithm are recommended for both Gaussian and aberrated response
shapes when operating at a proposed 5% error tolerance over a
specified range of overall response widths, test system scan rates,
and electro-optical signal generation levels.
Enhanced terahertz diffuse scattering through convolutional coding on broadband polarization conversion metasurface
Authors: Song Tianyang , Lan Feng , Wang Luyang , Yang Munan , Zeng Hongxin , Liu Wenxin , Mazumder Pinaki , Zhang Yaxin , Yang Ziqiang
Published: December 2024

Future 6 G systems integrating joint communication and sensing demand more attention to terahertz diffuse scattering. Despite coding metasurface exerting prevailing capabilities of regulating diffuse scattering of electromagnetic (EM) waves in a flexible digital manner, cost-effectiveness, non-structural reconfigurability, broadband, and wide-angle high-efficiency in terahertz range require further research. This paper proposes an ultra-wideband and high-efficiency reflective linear polarization conversion metasurface to reduce radar cross-section (RCS). Simulation results show that the polarization conversion ratio (PCR) is above 90% in an ultra-wideband from 0.24 THz to 0.52 THz, and the fractional bandwidth reaches 74%. Taking the advantages of high-efficiency and broad-bandwidth polarization conversion, the meta-element and its mirror-symmetry element form the 1-bit digital metasurface. Further comparative study shows the feasibility of enhancing the RCS performance by implementing a convolutional process among different diffusive coding patterns. The measured results show that the reflection amplitude of the three coding metasurfaces is less than -19 dB when the incident angle is 15°. Additionally, compared with the Golay-Rudin-Shapiro (GRS), the convolutional coding metasurface of GRS + Cross and GRS + Checkerboard effectively suppress specular reflection, achieving a maximum suppression amplitude of 17 dB. The proposed metasurface holds significant potential for manipulating terahertz waves, offering promising applications that contribute to RCS reduction, computational imaging, and multi-beam shaping.
Self-calibrating Fourier ptychographic microscopy using automatic differentiation
Authors: You Ruilin , Liang Rongguang
Published: December 2024

Fourier ptychographic microscopy (FPM) can provide high-throughput imaging by computationally combining low-resolution images at different spatial frequencies within the Fourier domain. The core algorithm for FPM reconstruction draws upon phase retrieval techniques, including methods such as the ptychographic iterative engine (PIE), regularized PIE (rPIE), and embedded pupil function FPM (EPRY-FPM). The calibration of the physical setup plays a crucial role in the quality of the reconstructed high space–bandwidth product (SPB) image. Despite advances, many methods, incorporating either machine learning or calibration algorithm, face challenges. These include the need for extensive parameter tuning and extra optical system information, hindering their practical use. To address these limitations, we introduce a novel, to the best of our knowledge, self-calibrating FPM reconstruction approach that utilizes automatic differentiation. This method diverges from traditional iterative phase and amplitude updates, opting instead to simultaneously recover a complex 2D image and refine the optical system’s physical parameters. Our approach matches the effectiveness of existing recovery techniques while significantly reducing the calibration burden. In this report, we will demonstrate our method is capable of self-calibrating without needing extra system information. We validate our algorithm’s performance through numerical simulations and then show its practicality by reconstructing a full field of view of cervical cell slides using ultraviolet Fourier ptychographic microscopy (UV-FPM).
Broadband hyperspectral LiDAR with a free-running gigahertz dual-comb supercontinuum
Authors: Camenzind Sandro , Nussbaum-Lapping Alexander , Willenberg Benjamin , Pupeikis Justinas , Taher Josef , Hakala Teemu , Kukko Antero , Hyyppä Juha , Ray Pabitro , Phillips Christopher , Keller Ursula
Published: December 2024

Hyperspectral LiDAR (HSL) enables the simultaneous acquisition of the surface geometry and spectral signatures of remote natural targets, making it valuable for various applications such as material probing, automated point cloud segmentation, and vegetation health monitoring. We present a first proof-of-concept study of a broadband dual-comb HSL system based on a 1-GHz dual-comb supercontinuum (SC). The SC spans from 820 to 1300 nm, generated via coherent spectral broadening of a free-running single-cavity dual-comb oscillator at 1053 nm in a single nonlinear photonic crystal fiber. The HSL system achieves a sub-μm ranging precision on a non-cooperative target at an update rate of 670 Hz. The shot-noise limited electronic dual-comb interferograms furthermore encode the spectral information of the target reflection across the SC bandwidth. This allows the capture of precise 3D point clouds with spectral signatures, unlocking new possibilities for spectrum-based material classification.
Distinct patterns of connectivity with the motor cortex reflect different components of sensorimotor learning
Authors: Areshenkoff Corson N. , de Brouwer Anouk J. , Gale Daniel J. , Nashed Joseph Y. , Smallwood Jonathan , Flanagan J. Randall , Gallivan Jason P.
Published: December 2024

Sensorimotor learning is supported by multiple competing processes that operate concurrently, making it a challenge to elucidate their neural underpinnings. Here, using human functional MRI, we identify 3 distinct axes of connectivity between the motor cortex and other brain regions during sensorimotor adaptation. These 3 axes uniquely correspond to subjects’ degree of implicit learning, performance errors and explicit strategy use, and involve different brain networks situated at increasing levels of the cortical hierarchy. We test the generalizability of these neural axes to a separate form of motor learning known to rely mainly on explicit processes and show that it is only the Explicit neural axis, composed of higher-order areas in transmodal cortex, that predicts learning in this task. Together, our study uncovers multiple distinct patterns of functional connectivity with motor cortex during sensorimotor adaptation, the component processes that these patterns support, and how they generalize to other forms of motor learning.
Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts
Authors: Mahmoudi Ikram , Quignot Chloé , Martins Carla , Andreani Jessica
Published: December 2024

Protein-RNA interactions play a critical role in many cellular processes and pathologies. However, experimental determination of protein-RNA structures is still challenging, therefore computational tools are needed for the prediction of protein-RNA interfaces. Although evolutionary pressures can be exploited for structural prediction of protein-protein interfaces, and recent deep learning methods using protein multiple sequence alignments have radically improved the performance of protein-protein interface structural prediction, protein-RNA structural prediction is lagging behind, due to the scarcity of structural data and the flexibility involved in these complexes. To study the evolution of protein-RNA interface structures, we first identified a large and diverse dataset of 2,022 pairs of structurally homologous interfaces (termed structural interologs). We leveraged this unique dataset to analyze the conservation of interface contacts among structural interologs based on the properties of involved amino acids and nucleotides. We uncovered that 73% of distance-based contacts and 68% of apolar contacts are conserved on average, and the strong conservation of these contacts occurs even in distant homologs with sequence identity below 20%. Distance-based contacts are also much more conserved compared to what we had found in a previous study of homologous protein-protein interfaces. In contrast, hydrogen bonds, salt bridges, and π-stacking interactions are very versatile in pairs of protein-RNA interologs, even for close homologs with high interface sequence identity. We found that almost half of the non-conserved distance-based contacts are linked to a small proportion of interface residues that no longer make interface contacts in the interolog, a phenomenon we term “interface switching out”. We also examined possible recovery mechanisms for non-conserved hydrogen bonds and salt bridges, uncovering diverse scenarios of switching out, change in amino acid chemical nature, intermolecular and intramolecular compensations. Our findings provide insights for integrating evolutionary signals into predictive protein-RNA structural modeling methods.
Different dry-wet pulses favor different functional strategies: A test using tropical dry forest tree species
Authors: Vega-Ramos Flor , Cifuentes Lucas , Pineda-García Fernando , Dawson Todd , Paz Horacio
Published: December 2024

In many terrestrial habitats, plants experience temporal heterogeneity in water availability both at the intra and inter annual scales, creating dry-wet pulse scenarios. This variability imposes two concomitant challenges for plants: surviving droughts and efficiently utilizing water when it becomes available, whose responses are closely interconnected. To date, most studies have focused on the response to drought following static designs that do not consider consequences of repeated transitions from one state to the other. In principle, different dry-wet pulse scenarios among years may differentially affect species performance, plant strategies, and promote coexistence through temporal niche separation. We predicted that short frequent droughts would disfavor drought-avoidant species, as rapid leaf loss and production could disrupt their carbon balance, whereas tolerant species, which maintain carbon gain during droughts, should thrive in such conditions. Prolonged droughts might harm tolerant species by causing severe cavitation. We assessed the survival and growth responses of seedlings from 19 tropical dry forest tree species to simulated natural dry-wet pulse scenarios, examining their relationships with the continuum of species’ functional strategies under field conditions, and used greenhouse experiments to accompany the field experiment. As expected, different dry-wet pulse scenarios favored different plant functional strategies. Contrary to predictions, the most tolerant outperformed the most avoiders under all drought scenarios, while rapid water-exploiters thrived under non-drought conditions. The superiority of tolerant over avoider species was reverted in the greenhouse, suggesting that in addition to physiology, the fate of species may depend on extrinsic factors as natural enemies. The interplay between the marked variability of dry-wet pulse scenarios across the years and the diversity of water use strategies may contribute to species coexistence in the tropical dry forests. This research is relevant in predicting changes in dominant tree species under future climate scenarios characterized by increased temporal variation in water availability.
Integrated study of Quercetin as a potent SARS-CoV-2 RdRp inhibitor: Binding interactions, MD simulations, and In vitro assays
Authors: Metwaly Ahmed M. , El-Fakharany Esmail M. , Alsfouk Aisha A. , Ibrahim Ibrahim M. , Elkaeed Eslam B. , Eissa Ibrahim. H.
Published: December 2024

To find an effective inhibitor for SARS-CoV-2, Quercetin’s chemical structure was compared to nine ligands associated with nine key SARS-CoV-2 proteins. It was found that Quercetin closely resembles Remdesivir, the co-crystallized ligand of RNA-dependent RNA polymerase (RdRp). This similarity was confirmed through flexible alignment experiments and molecular docking studies, which showed that both Quercetin and Remdesivir bind similarly to the active site of RdRp. Molecular dynamics (MD) simulations over a 200 ns trajectory, analyzing various factors like RMSD, RG, RMSF, SASA, and hydrogen bonding were conducted. These simulations gave detailed insights into the binding interactions of Quercetin with RdRp compared to Remdesivir. Further analyses, including MM-GBSA, Protein-Ligand Interaction Fingerprints (ProLIF) and Profile PLIP studies, confirmed the stability of Quercetin’s binding. Principal component analysis of trajectories (PCAT) provided insights into the coordinated movements within the systems studied. In vitro assays showed that Quercetin is highly effective in inhibiting RdRp, with an IC50 of 122.1 ±5.46 nM, which is better than Remdesivir’s IC50 of 21.62 ±2.81 μM. Moreover, Quercetin showed greater efficacy against SARS-CoV-2 In vitro, with an IC50 of 1.149 μg/ml compared to Remdesivir’s 9.54 μg/ml. The selectivity index (SI) values highlighted Quercetin’s safety margin (SI: 791) over Remdesivir (SI: 6). In conclusion, our comprehensive study suggests that Quercetin is a promising candidate for further research as an inhibitor of SARS-CoV-2 RdRp, providing valuable insights for developing an effective anti-COVID-19 treatment.