bluuebunny/crossref_metadata_2025 huggingface dataset:
Three‐Dimensional Evaluation of Changes in the Nose and Upper Lip After Secondary Alveolar Bone Grafting in Patients With Unilateral Cleft Lip and Palate
Authors: Deedklin Attapong , Pisek Araya , Kongsomboon Supaporn , Pisek Poonsak
Published: November 2024

Introduction

Alveolar bone grafting (ABG) influences facial soft tissue changes, but the precise effects on the nose and upper lip remain unclear. This study used three‐dimensional (3D) facial images to evaluate nose and upper lip alterations after ABG. We further enhanced the visualisation of these changes by generating 3D superimpositions, colour maps and deviation analyses of key critical landmarks in these regions.

Materials and Methods

Forty patients (8–20 years old) with non‐syndromic unilateral cleft lip and cleft palate (UCLP) underwent ABG using the iliac bone from September 2022 to September 2023. Three‐dimensional facial images were analysed 1 month before and 3 months after surgery to evaluate the spatial displacement of 18 nose and upper lip landmarks to assess changes after ABG. Colour maps were constructed, and 3D deviation analysis was also performed. Paired sample t tests and Wilcoxon's signed‐rank tests were used to analyse alterations.

Results

The 3D analysis uncovered significant forward movement on the cleft side only. This included nasal alar, alar curvature and subalar points. The labrale superius of the upper lip showed similar movement. Conversely, other landmarks showed minimal changes in all directions.

Conclusions

ABG can improve the nasal contour on the cleft side. After ABG, significant forward movement occurs in the cleft side of the nasal alar, alar curvature and subalar regions. Although these changes are minimal, they contribute to the overall improvement in facial aesthetics.
Student Perspectives of Access to Surgery Under General Anaesthetic in the Undergraduate Dental Curriculum
Authors: Macluskey Michaelina , Anderson Angela S. , McAllister Peter , Shepherd Simon D.
Published: November 2024

Introduction

Delivering dental graduates who are competent to carry out extractions and surgical extractions can be challenging. Access to general anaesthetic (GA) operating provides an opportunity not only for hands‐on experience but also to reinforce teaching in oral and maxillofacial surgery. The aim of this study was to determine what our final year students' perceptions were of exposure to GA operating lists.

Materials and Methods

This was a mixed‐methods prospective study involving an anonymous online questionnaire followed by a focus group. All final year students (n = 60) were invited to participate by email at the end of the academic year and involvement in the focus group was voluntary. Information collected included the type of surgery observed, clinical experience gained and their impression of the experience and whether it influenced career aspirations.

Results

Forty‐one students completed the questionnaire (68%) and 10 students participated in the focus group (17%). All students observed treatment under GA and 38 (93%) treated cases under GA. Thirty‐nine (95%) students attended an oral surgery list and 33 (80.5%) attended an OMFS list. Most students carried out deciduous extractions (78%) and 15% carried out dentoalveolar surgery. Treatment observed was primarily oncological (70%) and dentoalveolar cases (54%). Access to GA was well received by the students who felt it provided improved teaching opportunities and helped to conceptualise the didactic teaching on the subject and place their dentistry within a wider healthcare context. Some students indicated a desire to pursue a career in oral surgery (37%) or OMFS (10%).

Conclusion

The results presented here are indicative that students appreciate the learning opportunity afforded by the GA experience and our recommendation would be to perpetuate access to GA lists and the associated surgical exposure.
DNA Hypomethylation Is One of the Epigenetic Mechanisms Involved in Salt‐Stress Priming in Soybean Seedlings
Authors: Yung Wai‐Shing , Wang Qianwen , Chan Long‐Yiu , Wang Zhili , Huang Mingkun , Li Man‐Wah , Wong Fuk‐Ling , Lam Hon‐Ming
Published: November 2024

Salt‐stress priming enhances the tolerance of plants against subsequent exposure to a similar stress. Priming‐induced transcriptomic reprogramming is mediated by multiple epigenetic mechanisms, the best known of which is histone modifications. However, not much is known about other epigenetic responses. In this study, salt‐stress priming resulted in global DNA hypomethylation in the leaves of soybean seedlings. The DNA methyltransferase activities in primed seedlings were reduced, contributing to the overall DNA hypomethylation. Genes associated with the hypomethylated DNA regions in primed seedlings also showed a higher mean level of the active histone mark, histone 3 lysine 4 trimethylation (H3K4me3), and a lower mean level of the repressive histone mark, H3K4me2. Transcriptomic analyses supported that DNA hypomethylation played a role in fine‐tuning the chromatin status in primed seedlings to potentiate gene expressions. Motif and transcriptional network analyses revealed that DNA hypomethylation may facilitate the responses mediated by key transcription factors in the abscisic acid (ABA)‐dependent pathway. A pre‐treatment using a DNA methyltransferase inhibitor, 5‐azacytidine, could enhance salt tolerance in non‐primed soybean seedlings, similar to the priming effect, suggesting the role of DNA hypomethylation in salt‐stress priming. Overall, this research furthers our understanding of the epigenetic mechanisms involved in salt‐stress priming in soybean.
Multi‐Omics Analyses Offer Novel Insights into the Selection of Sugar and Lipid Metabolism During Maize Domestication and Improvement
Authors: Wu Di , Guan Le , Wu Yingxue , Wang Yang , Gao Ruiqi , Zhong Jianbin , Zhang Qiunan , Wang Shifeng , Zhang Xudong , Zhang Guochao , Huang Jun , Gao Yanqiang
Published: November 2024

Over thousands of years of domestication, maize has undergone significant environmental changes. Understanding the genetic and metabolic trace during maize evolution can better contribute to molecular breeding and nutrition quality improvement. This study examines the metabolic profiles and transcriptomes of maize kernels from teosinte, landrace, and maize accessions at 15 days post‐pollination. Differentially accumulated metabolites were enriched in sugar and lipid metabolism pathways. The metabolic selection profile exhibited four distinct patterns: continuous increases, constant decrease, initial decline or stability followed by an increase, and initial growth or stability followed by a subsequent decline. Sugars and JA were positive selection while LPCs/LPEs were negative selection during evolution. The expression level of genes related to sugar accumulation was significantly higher in maize, contrasting with enhanced glycolysis and lipid metabolism activity in teosinte. The correlation network highlighted distinct hormonal regulation of sugar and lipid metabolism. We identified 27 candidate genes associated with sugar, lipid, and JA that have undergone strong selection by population genomic regions. The positive selection of the PLD may explain the negative selection of LPCs/LPEs due to substrate competition. These findings enhance our understanding of the evolutionary trajectory of primary metabolism in maize and provide valuable resources for breeding and improvement.
A New Approach to Reduce the Position Data of Moving Objects Using Neural Network
Authors: Diri Samet , Yildirim Mehmet
Published: November 2024

In this study, an ANN‐based Global Navigation Satellite System (GNSS) location data reduction approach was proposed. As GNSS location data becomes more common, efficient data reduction techniques are needed to reduce transmission, storage, and processing costs. This involves selecting key points from the original trajectory to maintain integrity, eliminating redundancy, and lowering transmission and storage expenses. In this study, we proposed a new method for reducing GNSS location data in both online and offline settings, utilizing an ANN trained with a mathematically generated dataset. ANN has not been used in data reduction in the literature. The approach involves training the ANN with a window size of 3 and a threshold value of 10°, followed by using the trained model for data reduction. Experimental results show that the ANN achieves a reduction rate of around 59.18% compared to the original trajectory. Notably, the ANN yields a significantly lower RMSE compared to a mathematical method, particularly in areas requiring precision. Despite the slightly slower computation times, the ANN remains suitable for real‐time applications, demonstrating its efficacy for GNSS location data reduction. Our study highlights its online capability, reasonable reduction rates, and low RMSE values, distinguishing it from existing literature. This method shows potential for scenarios where balancing reduction rates with data quality is crucial.
Pamplona, ciudad intermedia y universitaria en un entorno nacional, regional y binacional
Authors: Castelblanco Ramírez Hernán
Published: November 2024

El artículo tiene como objetivo contribuir al conocimiento de las interacciones ciudad intermedia y universidad teniendo como marco geográfico la ciudad de Pamplona Norte de Santander y su incidencia como centro subregional-nodal con vocación en la provisión de servicios transversales entre ellos el de educación superior. Se analiza la ciudad en el contexto de la geografía de los servicios y desde su condición de ciudad universitaria, a través de procesos socio territoriales, con el fin de caracterizar actividades, oportunidades e interacciones en el ámbito institucional, económico y cultural en el territorio. Como producto de investigación, pretende aportar en el entendimiento de las formas de producir ciudad, bajo dos supuestos: 1) las universidades como equipamiento urbano tienen un gran impacto, socioeconómico en el crecimiento y expansión urbana, 2) las universidades están ligadas de manera indisoluble con la ciudad, en hechos y lugares físicos que las convierten invariablemente en realidades socioespaciales.
EZH2 directly methylates PARP1 and regulates its activity in cancer
Authors: Meng Qingshu , Shen Jiangchuan , Ren Yanan , Liu Qi , Wang Rui , Li Qiaqia , Jiang Weihua , Wang Quan , Zhang Yixiang , Trinidad Jonathan C. , Lu Xiaotong , Wang Tingyou , Li Yanqiang , Yum Chaehyun , Yi Yang , Yang Yongyong , Zhao Dongyu , Harris Clair , Kalantry Sundeep , Chen Kaifu , Yang Rendong , Niu Hengyao , Cao Qi
Published: November 2024

DNA repair dysregulation is a key driver of cancer development. Understanding the molecular mechanisms underlying DNA repair dysregulation in cancer cells is crucial for cancer development and therapies. Here, we report that enhancer of zeste homolog 2 (EZH2) directly methylates poly(adenosine diphosphate–ribose) polymerase-1 (PARP-1), an essential enzyme involved in DNA repair, and regulates its activity. Functionally, EZH2-catalyzed methylation represses PARP1 catalytic activity, down-regulates the recruitment of x-ray repair cross-complementing group-1 to DNA lesions and its associated DNA damage repair; on the other hand, it protects the cells from nicotinamide adenine dinucleotide overconsumption upon DNA damage formation. Meanwhile, EZH2-mediated methylation regulates PARP1 transcriptional and oncogenic activity, at least in part, through impairing PARP1-E2F1 interaction and E2F1 transcription factor activity. EZH2 and PARP1 inhibitors synergistically suppress prostate cancer growth. Collectively, our findings uncover an insight of EZH2 functions in fine-tuning PARP1 activity during DNA damage repair and cancer progression, which provides a rationale for combinational targeting EZH2 and PARP1 in cancer.
Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma
Authors: Tarantino Giuseppe , Ricker Cora A. , Wang Annette , Ge William , Aprati Tyler J. , Huang Amy Y. , Madha Shariq , Chen Jiajia , Shi Yingxiao , Glettig Marc , Feng Catherine H. , Frederick Dennie T. , Freeman Samuel , Holovatska Marta M. , Manos Michael P. , Zimmer Lisa , Rösch Alexander , Zaremba Anne , Livingstone Elisabeth , Jameson Jacob C. , Saghafian Soroush , Lee Andrew , Zhao Karena , Morris Luc G.T. , Reardon Brendan , Park Jihye , Elmarakeby Haitham A. , Schilling Bastian , Giobbie-Hurder Anita , Vokes Natalie I. , Buchbinder Elizabeth I. , Flaherty Keith T. , Haq Rizwan , Wu Catherine J. , Boland Genevieve M. , Hodi F. Stephen , Van Allen Eliezer M. , Schadendorf Dirk , Liu David
Published: November 2024

The introduction of immune checkpoint blockade (ICB) has markedly improved outcomes for advanced melanoma. However, many patients develop resistance through unknown mechanisms. While combination ICB has improved response rate and progression-free survival, it substantially increases toxicity. Biomarkers to distinguish patients who would benefit from combination therapy versus aPD-1 remain elusive. We analyzed whole-exome sequencing of pretreatment tumors from four cohorts (
n
= 140) of ICB-naïve patients treated with aPD-1. High genomic heterogeneity and low ploidy robustly identified patients intrinsically resistant to aPD-1. To establish clinically actionable predictions, we optimized and validated a predictive model using ploidy and heterogeneity to confidently identify (90% PPV) patients with intrinsic resistance to and worse survival on aPD-1. We further observed that three of seven (43%) patients predicted to be intrinsically resistant to single-agent PD-1 ICB responded to combination ICB, suggesting that these patients may benefit disproportionately from combination ICB. These findings highlight the importance of heterogeneity and ploidy, nominating an approach toward clinical actionability.
Load sharing and accumulated bond fracture in ion-irradiated carbon mat for energy dissipation
Authors: Xiao Kailu , Wu Xianqian , Sang Zhen , Subramanian Vivek , Thomas Edwin L.
Published: November 2024

Multiwalled carbon nanotube (MWNT) aerogel mats were irradiated with carbon ions to explore the effect of irradiation-induced sp
3
bonds and sp
2
bond defects on ultrahigh strain rate mechanical properties. Energy dissipation was measured using a microprojectile impact test. Specific penetration energy

E
p
*

increased strongly with irradiation with a maximum

E
p
*

of ~26 megajoules per kilogram, over 200% higher than the previous best energy-absorbing material of pristine MWNT mats and at least an order of magnitude higher than any other material tested at the microscale. Perforation morphologies observed by electron microscopy show that a much larger network region is deformed due to sp
3
bond enhanced load sharing within and between tubes, while defects introduced by the radiation induce more bond, shell, and tube damage leading to strongly enhanced energy dissipation.
Rhodium-catalyzed atropodivergent hydroamination of alkynes by leveraging two potential enantiodetermining steps
Authors: Mi Ruijie , Wu Rongkai , Jing Jierui , Wang Fen , Li Xiao-Xi , Hong Xin , Li Xingwei
Published: November 2024

A pair of enantiomers is known to have different biological activities. Two catalysts with opposite chirality are nearly always required to deliver both enantiomeric products. In this work, chiral rhodium(III) cyclopentadienyl complexes are repurposed as efficient catalysts for enantiodivergent and atroposelective hydroamination of sterically hindered alkynes. Products with opposite chirality have been both obtained using the same or closely analogous chiral catalyst in good efficiency and excellent enantioselectivity, and the enantiodivergence was mainly enabled by an achiral carboxylic acid and its silver salt. Mechanistic studies revealed the origin of the enantiodivergence ascribable to the switch of the enantiodetermining step (alkyne insertion versus protonolysis) under acid control, which constitutes a previously unidentified working mode of enantiodivergence by leveraging two elementary steps.
The force has limits: Molecular motors in robotics
Authors: Hess Henry , Katira Parag , Rodriguez Juan B.
Published: November 2024

Molecular motors generate force to individually power molecular machines or collectively drive macroscopic actuators. The force output of molecular and macroscale motors appears to be constrained by the same scaling law relating motor force and mass. Here, potential origins of these universal performance characteristics are discussed and the implications examined.
Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels
Authors: Luu Minh Tri , Berengut Jonathan F. , Li Jiahe , Chen Jing-Bing , Daljit Singh Jasleen Kaur , Coffi Dit Glieze Kanako , Turner Matthew , Skipper Karuna , Meppat Sreelakshmi , Fowler Hannah , Close William , Doye Jonathan P. K. , Abbas Ali , Wickham Shelley F. J.
Published: November 2024

In cells, proteins rapidly self-assemble into sophisticated nanomachines. Bioinspired self-assembly approaches, such as DNA origami, have been used to achieve complex three-dimensional (3D) nanostructures and devices. However, current synthetic systems are limited by low yields in hierarchical assembly and challenges in rapid and efficient reconfiguration between diverse structures. Here, we developed a modular system of DNA origami “voxels” with programmable 3D connections. We demonstrate multifunctional pools of up to 12 unique voxels that can assemble into many shapes, prototyping 50 structures. Programmable switching of local connections between flexible and rigid states achieved rapid and reversible reconfiguration of global structures in three dimensions. Multistep assembly pathways were then explored to increase the yield. Voxels were assembled via flexible chain intermediates into rigid structures, increasing yield up to 100-fold. We envision that foldable chains of DNA origami voxels can achieve increased complexity in reconfigurable nanomaterials, providing modular components for the assembly of nanorobotic systems with future applications in synthetic biology, assembly of inorganic materials, and nanomedicine.
Tracing carbonatite metasomatism in the source of arc magmatism using Li-Mg-Zn isotopes: Implications for deep carbon cycling
Authors: Yan Xiang-Yu , Yang De-Bin , Xu Wen-Liang , Wang Feng , Wang Chun-Guang , Wang An-Qi
Published: November 2024

The subduction of carbonate-bearing components into Earth’s interior is a key part of the deep carbon cycle. However, the mechanisms of carbon transfer from the subducted slab to the sub-arc mantle remain unclear. Here we present a novel study using the Li-Mg-Zn isotopic systematics of Early Cretaceous olivine websterites from the northeastern North China Craton, China, to investigate cryptic carbonatite metasomatism. Clinopyroxene in the websterites has high Ca/Al and (La/Yb)N ratios, indicating their derivation from fluxed melting of a carbonated mantle peridotite. The samples exhibit lighter Li (δ7Li = −4.42‰ to 3.62‰) and Mg (δ26Mg = −0.40‰ to −0.36‰) isotopic compositions compared with the mantle, but similar Zn (δ66Zn = 0.25‰−0.29‰) isotopic compositions, suggesting the source was modified by ∼14% dehydrated altered oceanic crust and ∼6% carbonate-bearing silicate sediments. We propose that arc magmatism lacking high-δ7Li and -δ66Zn signatures does not necessarily indicate the absence of carbonates in the source. The combination of clinopyroxene and Li-Mg-Zn isotopic analyses can provide an improved understanding of deep carbon cycling.
Supplemental Material: Detrital thermochronology histories preserved in Paleogene strata of Utah (USA) provide distant records of Paleozoic Alleghanian orogenesis and sediment dispersal
Authors: Stevens Goddard Andrea , al. et
Published: November 2024

Analytical and modeling methods and datasets.  
Coronary microvascular function and atherosclerotic plaque burden in ischaemia and no obstructive coronary arteries: a secondary analysis of the CorMicA trial
Authors: Ang Daniel TY , Carberry Jaclyn , Ford Thomas J , Kamdar Anna , Sykes Robert , Sidik Novalia P , Carrick David , McCartney Peter J , Collison Damien , Robertson Keith , Shaukat Aadil , Rocchiccioli J Paul , McGeoch R , Watkins Stuart , Hood Stuart , McEntegart Margaret , Lindsay Mitchell , Eteiba Hany , Oldroyd Keith G , Good Richard , McConnachie Alex , Berry Colin
Published: November 2024

Background

The relationship between atherosclerosis and endotypes of myocardial ischaemia with no obstructive coronary artery disease (INOCA) is unclear. We investigated potential associations between cumulative atherosclerotic plaque burden quantified using the Gensini score, novel invasive indices of coronary microvascular function (microvascular resistance reserve (MRR); resistive reserve ratio (RRR)) and related INOCA endotypes.

Methods

Coronary angiography and invasive coronary function tests were simultaneously acquired in the CorMicA cohort. A comprehensive physiological assessment was performed using both a thermodilution-based diagnostic guidewire and intracoronary acetylcholine provocation testing. Angiograms were examined for luminal stenosis in each segment of the SYNTAX coronary model. Cumulative plaque burden was quantified using the Gensini score, which incorporated both the number of diseased coronary segments and stenosis severity. Results were compared with indices of microvascular function and INOCA endotypes. Angiographic analyses were performed blind to coronary physiology findings.

Results

In 151 participants (median age 61 years; 73.5% female) without flow-limiting coronary artery disease, medical history included 41.7% smoking, 63.6% hypertension and 19.2% diabetes mellitus. The left anterior descending artery underwent diagnostic guidewire testing in 85.4%, and 55.0% of participants had abnormal coronary flow reserve (CFR) and/or Index of Microcirculatory Resistance (IMR). The median Gensini score was 6.0 (IQR 2.5–11.0). CFR (p=0.012), MRR (p=0.026) and RRR (p=0.026), but not IMR (p=0.445), were univariably associated with raised Gensini scores. These significant effects persisted in multivariable models controlling for potential confounders. Considering INOCA endotypes, Gensini scores differed among participants with microvascular angina (MVA) (7.0 (2.5–11.0)), vasospastic angina (VSA) (4.5 (2.0–10.0)), mixed MVA/VSA (9.0 (5.0–11.5)) and non-cardiac symptoms (3.5 (1.5–8.0)); Kruskal-Wallis p=0.030.

Conclusions

Reduced CFR, MRR and RRR, and MVA were associated with increased coronary atherosclerotic plaque burden, as evidenced by higher Gensini scores. These novel findings provide a mechanistic link between INOCA and cardiovascular events, reinforcing the importance of antiatherosclerosis therapy in patients with MVA.
Surgical and transcatheter aortic valve interventions for aortic stenosis in England: sociodemographic variations in treatment trends and outcome over 20 years
Authors: Singh Anvesha , Chalmers Fionna , Aslam Saadia , Bolton Thomas , Stevenson Anna , Squire Iain , Khunti Kamlesh , McCann Gerry P , Lawson Claire
Published: November 2024

Background

Health inequalities in cardiovascular care have been identified in the UK. The sociodemographic characteristics of patients undergoing intervention for aortic stenosis (AS) in England, and the impact of COVID-19, is unknown.

Methods

National linked data sets identified all surgical aortic valve replacement (SAVR) and transcatheter aortic valve implantation (TAVI) for AS, and post-intervention cardiovascular mortality, between 2000 and 2023.

Results

Of 179 645 procedures, there were 139 990 SAVR (mean age 71±10.8 years, 64% male, 96.0% white) and 39 655 TAVI (mean age 81±7.7 years, 57% male, 95.7% white). Rates of SAVR declined during COVID-19 for all groups, but TAVI rates increased steadily. Women were older; ethnic minority groups and those from most deprived areas were younger, with greater comorbidities. Women and more deprived groups had lower rates of SAVR (age-standardised rates per 100 000 in 2020–2023: 17.07vs6.65 for menvswomen; 9.82vs10.10 for Index of Multiple Deprivation (IMD)-1vsIMD-5) and TAVI (20.20vs9.79 for menvswomen; 9.55vs13.36 for IMD-1vsIMD-5). These discrepancies widened over time. Ethnic differences were observed for SAVR, with the lowest rates in black patients. Cardiovascular mortality post-intervention was lower in female patients and with decreasing deprivation, with no ethnicity-based differences.

Conclusions

There are differences in intervention rates for AS in England, with lower rates in female patients and to a lesser extent, those from the most deprived areas and ethnic minority groups. These variations have widened over time. Post-intervention cardiovascular mortality is lower in women and with decreasing deprivation. Public health measures and research are needed to identify the true prevalence of AS in different populations, and the reasons for potential inequalities.
Weaving ways of knowing in practice: a collaborative approach to prioritizing community knowledge and values in wildlife camera monitoring with Magnetawan First Nation
Authors: Kemp Claire , Yarchuk Kathryn , Menzies Allyson , Perron Nadine , Noganosh Samantha , Northrup Joseph , Popp Jesse
Published: November 2024

There is not one singular way to weave together Indigenous and Western knowledges; creating meaningful cross-cultural collaborations requires a foundation of relationships rooted in the context of specific people and place. As interest in working across knowledge systems increases, our goal is to provide an example of respectful and appropriate cross-cultural collaboration within environmental practice. We demonstrate our collaborative, mixed-methods approach to developing a community-based wildlife monitoring program with Magnetawan First Nation that prioritizes community knowledge and values. Through community interviews and a youth sharing circle, participants highlighted values (respect, interconnection, reciprocity, collaboration, and relationship) as well as research priorities, providing examples of what each may look like in practice, to inform our monitoring approach. These examples, paired with reflections from the research team, are shared to explore the process of weaving together knowledge and values to co-create a community-based wildlife monitoring program, applying wildlife cameras as much more than simply a tool for data collection. This research provides tangible examples of weaving together knowledges and values in the context of environmental monitoring, helping guide future cross-cultural collaboration to ensure this work is being done in a good way.
About this title - The Peter Fookes Engineering Geological Legacy in Geomodels, Geomaterials and Geomorphology
Authors: Griffiths J. S. , Giles D. P. , Davis J. A. , Dunlop J. J.
Published: November 2024

This book commemorates the life, work and heritage of Professor Peter Fookes (1933–2020) who worked in over 100 countries and produced some 200 publications. He was the recipient of the William Smith and Glossop medals and was renowned for his pioneering work in engineering geomorphology, geomaterials and the development of ground models for engineering geology.
Mountain road engineering: the legacy of Peter Fookes across the continents
Authors: Hearn Gareth , Martin Richard
Published: November 2024

Peter Fookes played a pioneering role in many fields of engineering geology, but the legacy of his work in mountain regions, and especially with respect to the design of mountain roads, was among his most lasting. In the 1970s, he took on the challenge of assembling and leading a team of geo-specialists to assist in the design and construction of the Dharan-Dhankuta Road (DDR) through intensely dissected fold mountain terrain in east Nepal. Peter did not fail to deliver, and the mountain model he produced to accommodate the complexity and dynamic nature of the terrain helped guide project decision-making and design. Peter's awareness of the need to understand the geological and geomorphological history of any site led to the
Total Geology Approach
that offered a blueprint for engineering geological practitioners thereafter. The authors describe a project to construct a road across the Blue Nile gorge in Ethiopia where this blueprint was applied. Design and construction of the DDR and the road across the Blue Nile gorge were especially demanding. To date both roads have performed relatively successfully since they were opened to traffic and are fitting tributes to Peter's legacy.
Recognition of Counterfactual Statements in Turkish
Authors: Acar Ali , Tekir Selma
Published: November 2024

Counterfactual statements are examples of causal reasoning as they describe events that did not happen and, optionally, those events’ consequences if they happened. SemEval-2020 introduces the counterfactual detection (CFD) task and shares an English dataset. Since then, a set of datasets has been released in English, German, and Japanese as part of Amazon product reviews. This work releases the first Turkish corpus of counterfactuals (TRCD). The data collection process is driven by a clue phrase list of counterfactuals, mainly in the form of verb inflections in Turkish. We use clue phrase-based filtering to collect sentences from the Turkish National Corpus (TNC). On the other hand, half of the collection is subject to random word filtering to avoid selection bias due to clue phrases. After the human annotation process with an Inter Annotator Agreement of 0.65, we have 5000 sentences, of which 12.8% contain counterfactual statements. Furthermore, we provide a comprehensive baseline of transformer-based models by testing the effect of clue phrases, cross-lingual performance comparisons using the available CFD datasets, and zero-shot cross-lingual classification experiments using fine-tuning on the different combinations of the existing datasets. The results confirm that TRCD is compatible with the other CFD datasets. Moreover, fine-tuning a Turkish-specific model (BERTurk) performs better than the multilingual alternatives (mBERT and XLM-R). BERTurk is more robust to clue phrase masking. This result emphasizes the importance of a language-specific tokenizer for contextual understanding, especially for low-resource languages. Finally, our qualitative analysis gives insights into errors by different models.
A Case Report on 13q12.3 Microdeletion Syndrome Caused by HMGB1 Haploinsufficiency
Authors: Wen Ting , Shayota Brian J. , Wallace Lauren , Mani Coumarane , Davis Neal , Zhao Jian
Published: November 2024

Heterozygous microdeletions at 13q12.3 are associated with a rare genetic disorder, 13q12.3 microdeletion syndrome, characterized by intellectual disability, microcephaly, development delay, facial dysmorphisms, atopy, and obesity. Reported 13q12.3 microdeletions vary in size and typically encompass multiple genes. Previous studies have defined a minimal overlap region of 13q12.3 microdeletions and suggested that most of the phenotype associated with the 13q12.3 microdeletion syndrome could be attributed to the loss of the high mobility group box 1 (HMGB1) gene within the overlap region. Here, we report a pediatric patient who had typical phenotypic features of 13q12.3 microdeletion syndrome, including motor and moderate speech developmental delays, microcephaly, and severe atopy, along with anxiety and aggressive behaviors. Trio‐based microarray analysis identified a 62‐kb apparently de novo heterozygous deletion at 13q12.3 in the proband, fully encompassing all coding exons of the HMGB1 gene yet not affecting any other neighboring genes. This case report presents a rare HMGB1 single‐gene deletion in a patient with classic features of 13q12.3 microdeletion syndrome, allowing a better delineation of clinical phenotypes associated with the loss of HMGB1. Our findings, together with previous reports, strongly support the pathogenic role of HMGB1 haploinsufficiency in the 13q12.3 microdeletion syndrome.
Incidental Radiological Finding of an Intravenous Needle in a Pediatric Cervical Spine
Authors: Namer Thana , Alanazi Rahaf , Al Karawi Maryam , Saeed Mahfood , Al Karawi Sarmad
Published: November 2024

Cases of cervical foreign bodies are considered rare, and cases of needle that have migrated into the spinal canal are fairly uncommon. The most well‐documented cases are those of acupuncture needles. We present a case of an incidental finding of an intravenous needle extending posteriorly between C7 and T1 interspinous space and ending at the level of C5‐C6 interspace in a 2‐year‐old boy. We discuss the possible port of entry and the management of such findings.
∗‐π‐Reversible ∗‐Semirings and Their Applications to Generalized Inverses
Authors: Zhuo Yuanfan , Gu Qinqin
Published: November 2024

We introduce and study a new class of ∗‐semirings which is called ∗‐π‐reversible ∗‐semirings. A ∗‐semiring R is said to be ∗‐π‐reversible if for any a, b ∈ R, ab = 0 implies there exist two positive integers m and n such that . Some characterizations and examples of this class of semirings are given. As applications, generalized inverses related to ∗‐π‐reversible ∗‐semirings are studied. For an additive cancellative, Id‐complemented and ∗‐π‐reversible ∗‐semiring R, if a ∈ R is reflexive invertible, some equivalent characterizations of a being normal elements and strong EP elements are given.
Table S6 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

MET sites
Table S2 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Peptide MALDI Peak List
Table S1 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Glycan Peak List
Supplementary Data Figure Legends from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Figure Legends for Supplementary Data
Figure S9 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Segmentation Analysis of tissues according to N-glycan analysis
Figure S18 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Table of biomarker candidates
Figure S14 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Annotated LCMS spectra for COL1A1;COL1A2
Figure 4 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Statistical analysis of detected N-glycans in each category of TMA following EndoF3 and PNGaseF digestion. A,t test plot of detected N-glycans following EndoF3 digestion. Structures shown for top 10 most significant N-glycans (B) t test plot of detected N-glycans following PNGaseF digestion. Structures shown for top 10 most significant N-glycans C, Left-Right: PCA, PLS-DA plots for detected N-glycans following EndoF3 digestion. ROC curve showing NED vs. MET after EndoF3 digestion D, Left-Right: PCA, PLS-DA plots for detected N-glycans following PNGaseF digestion. ROC curve showing NED vs. Mets after PNGaseF digestion.
Figure 2 from Determining the N-Glycan and Collagen/Extracellular Matrix Protein Compositions in a Novel Outcome Cohort of Prostate Cancer Tissue Microarrays Using MALDI-MSI
Authors: Hartig Jordan P. , Bejar Kaitlyn , Young Lyndsay E.A. , Grimsley Grace , Bethard Jennifer R. , Troyer Dean A. , Hernandez Javier , Wu Jennifer D. , Ippolito Joseph E. , Ball Lauren E. , Gelfond Jonathan A.L. , Johnson-Pais Teresa L. , Mehta Anand S. , Leach Robin J. , Angel Peggi M. , Drake Richard R.
Published: November 2024

Glycan imaging data from TMA comparing metastasis vs. no recurrence. A, MALDI-MSI images of TMAs from metastasis (MET) category and no recurrence (NED) category. N-glycan images representative of differentiating expression of select N-glycan categories, followed by segmentation analysis of 152 detected N-glycans. B–I, Box plot and ROC curves for each category of N-glycan detected within each group of TMAs. t test results shown on each boxplot.
Visual outcomes after spontaneous and surgical closure of small idiopathic macular holes: a comparative study
Authors: Toumi Elsa , Guindolet Damien , Bonnin Sophie , Bruneau Sébastien , Leflot Marie , Duvillier Amélie , Lejoyeux Raphaël , Tadayoni Ramin
Published: November 2024

Introduction. Small full-thickness macular holes (FTMHs) are classically treated surgically but can also occasionally close spontaneously. Long-term visual outcomes of spontaneously closed FTMHs are not well described. We compared best-corrected visual acuity (BVCA) after surgical and spontaneous closure of idiopathic FTMH (IMHs) and assessed the effect of IMH size on BCVA.
Methods. This retrospective study was performed at Rothschild Foundation Hospital, Paris, France, from January 2015 to June 2021. The study included patients with small IMH, i.e. ≤ 250 m, divided into spontaneously closed IMH (SIMH) and surgically closed IMH. Both groups were divided into 3 subgroups according to IMH diameter: < 100 m, 100-150 m, or 151-200 m.
Results. A total of 109 patients had surgical IMH closure and 18 spontaneous IMH closure. Among all the patients of the study, we observed 17% of spontaneous closure. All SIMHs were < 250 m. The groups did not differ in final BCVA or BCVA gain. BCVA significantly improved after surgery whatever the IMH size. In SIMH group, final BCVA did not differ by IMH size. In the 100-150 m subgroups, BCVA gain was significantly greater for the surgical closure compared to the SIMH groups (-0.35) ±0.2 vs -0.16) ±0.2 logMAR; p=0.01).
Conclusion. Vision results are similar between spontaneously closed and surgically closed macular holes. Spontaneous closure of macular holes can occur, it is therefore reasonable to consider observation before macular hole surgery.
A Report of Dual Presentations of Pseudo-TORCH Syndrome 1 and MCC2 Deficiency and Review of the Literature
Authors: Talea Ali , Bayat Shiva , Shahbodagh Khan Golazin , Pak Neda , Aziz-Ahari Solmaz , Sinaei Roya , Tavasoli Ali Reza , Ashrafi Mahmoud Reza , Heidari Morteza
Published: November 2024

Introduction: Pseudo-TORCH syndrome, named as such due to the mimicry of intrauterine TORCH infections in the absence of infection, is a neurological disorder presenting primarily with congenital microcephaly, intracranial calcifications, simplified gyration and polymicrogyria, and severe developmental delay, which can be attributed to variants in the OCLN gene. MCC2 deficiency, a neurometabolic disorder due to impairments in the catabolism of Leucine, with highly variable clinical presentations in addition to landmark metabolic features is put down to variants in MCCC2 gene. Case Presentation: Known as independent conditions, the intriguing presence of dual manifestations in a 3.5-year-old boy was investigated in the study. The patient was referred to our Myelin Disorders Clinic due to congenital microcephaly, developmental regression, and medication-resistant epilepsy. WES was performed on patient’s samples for variant detection and subsequent confirmation. Bioinformatics analysis was performed for prioritization and validation according to the standard criteria. The resultant findings were consequently confirmed in the proband and his parents by Sanger sequencing. WES revealed the presence of two concurrent variants in OCLN and MCCC2 on the same chromosome, chromosome 5, both in homozygous state in the proband. Both variants are classified as pathogenic according to ACMG classification system having been previously reported in the literature. Conclusion: The two variants observed in our patient, a homozygous missense change and a homozygous deletion interestingly occurring on the same chromosome, lead us to think that either these two conditions may be totally independent of each other, having co-occurred by chance, or there may be an underlying association between the two variants, rendering their co-occurrence as a haplotype more possible.
Similarities and differences in diurnal salivary adrenal hormones in monozygotic twins with discordant birthweight
Authors: Roedig Thea , Eberhardt Nora , Bartmann Peter , Schreiner Felix , Holterhus Paul-Martin , Kulle Alexandra E. , Schulte Sandra , Gohlke Bettina
Published: November 2024

Introduction
DHEAS is increased in formerly small-for-gestational-age singletons and in smaller twins compared to their normal-weight co-twin. Less is known concerning other adrenal hormones. We compared diurnal salivary profiles in monozygotic twins with intra-twin birthweight(bw)-differences to analyse the long-term impact of bw and persistent intra-twin auxological differences on various adrenal hormones.

Methods
46 monozygotic pre-pubertal twin-pairs with bw-difference of <1SDS (concordant; n=29, 13 female) and ≥1SDS (discordant; n=17, 6 female) were recruited. At a mean age of 6.9 years (yrs) saliva samples were collected (7 am/waking, 1 pm, 6 pm, and 9 pm) and analysed with liquid chromatography-tandem mass spectrometry.

Results
Diurnal salivary concentrations showed significant intra-twin correlations in all twin-pairs for nearly all time-points: progesterone and androstenedione (4/4 time-points), 17-hydroxyprogesterone (2/4). However, in the discordant group mean progesterone differed significantly (p=0.018) between the smaller (3.27nmol/L, SD 3.87) and the larger twin (0.72nmol/L, SD 0.42) at 7 am and intra-twin differences were observed at 3/4 time-points. Regression analyses of intra-twin differences confirmed that actual hormonal parameters were explained mainly by the co-twin parameter. However, at 6 pm progesterone concentration of the smaller twin was explained by bw (Β -1.102; SE 0.563; p=0.05) and actual weight (Β 0.799; SE 0.327; p=0.019).

Conclusion
The significant correlations within monozygotic twin-pairs in all measured hormones at nearly all time-points suggest a strong genetic influence on the adrenal axis. Among the discordant twin pairs, we found significant variations in progesterone, suggesting additional long-lasting influence from intrauterine conditions on adrenal hormones with possible metabolic consequences.

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Perineural invasion for risk stratification in cutaneous squamous cell carcinoma: a scoping review
Authors: Crüts Emmy C. , Moermans Myrthe M.G. , Abdul Hamid Myrurgia , Nelemans Patty J. , Mosterd Klara
Published: November 2024

Introduction: Microscopic perineural invasion (mPNI) is a histopathological characteristic that can be found in cutaneous squamous cell carcinoma (cSCC). In the eight edition of the American Joint Committee on Cancer (AJCC), mPNI defined as the involvement of nerves ≥0.1mm and nerves deeper than the dermis is included in risk stratification of cSCC. The question remains whether other mPNI features are important for optimal cSCC staging. We aim to summarize the evidence from published studies on the independent association between various mPNI features and the risk of recurrence, metastasis and disease-specific death in patients with cSCC.
Methods: Embase, PubMed, and Web of Science were searched from January 2023 to February 2024 to identify studies that reported the prognostic impact of mPNI features in patients ≥18 years with histopathologically verified cSCC. Data on study and tumour characteristics were extracted.
Results: Nineteen studies met the inclusion criteria and evaluated one or more mPNI features in cSCC including nerve diameter, the extent of mPNI, the number of affected nerves, and depth of mPNI. Two studies provided evidence that ‘mPNI ≥0.1mm’ and ‘mPNI deeper than the dermis’ are significantly and independently associated with poor prognosis after correction for other mPNI features and high-risk factors. One of these studies additionally identified ‘involvement of ≥3 nerves’ as an independent and significant predictor of higher risk of local recurrence (HR, 2.17; 95% CI, 1.03-4.56; p=0.04).
Conclusion: Besides ‘nerve diameter of ≥0.1mm’ and ‘depth of mPNI involvement’, ‘involvement of multiple nerves’ was found to be an independent risk factor for poor prognosis and should also be considered for appropriate risk stratification.