bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Healthy Diet for Beginning Readers: Decodable Texts as Part of a Comprehensive Literacy Program
Authors: Pennell Ashley E. , Jordan Rebecca Lee Payne , Nash Kindel Turner , Elson Kerry , Trathen Woodrow 
Published: February 2024

AbstractWe suggest that a healthy literacy diet for beginning readers consists of literacy experiences along a number of dimensions, including experiences with decodable text. As such, this article explores the role of decodable texts in a comprehensive early literacy curriculum that recognizes literacy as a complex, culturally mediated, and multifaceted set of skills. We provide five guidelines for practitioners to use when evaluating decodable texts to be used with beginning readers. As an example of the type of analysis we recommend for selecting quality decodable text, we examine one decodable text for its merit in fulfilling the guidelines described in this article.
Image‐based detection and classification of plant diseases using deep learning: State‐of‐the‐art review
Authors: Bagga Manju , Goyal Sonali 
Published: February 2024

AbstractPlant diseases are assumed to be one of the primary causes regulating food manufacturing and reducing deficits in crop yield, and it is crucial that plant diseases have rapid spotting and identification. Since the demand for food is rising quickly due to population growth, the main issue for any country is plant disease mechanization in agricultural science. Recent developments in deep learning techniques have found use in plant disease recognition, offering a robust tool with exceedingly precise results. Our main goal is to employ deep learning mechanisms to better understand diseases and how to identify them quickly. In this regard, we analyzed 94 publications chosen from the last 7 years (2016–2023) that show how CNN's philosophy has evolved over this period with various approaches to treating plant diseases. Furthermore, a full description of numerous crops, diseases connected to them, various datasets relating to plant diseases, existing CNN models, and customized CNN architectures is provided. The results of this state‐of‐the‐art review can be implemented to comprehend the cutting‐edge trends in the application of deep learning (CNNs) to detect plant diseases as well as pinpoint any research gaps that require the scientific community's attention.
Parallel Normal Fields
Authors: Pinkall Ulrich , Gross Oliver 
Published: February 2024

AbstractFor curves $$\gamma \colon [a,b] \to \mathbb {R}^n$$
γ
:
[
a
,
b
]
→

ℝ

n

there is an analog $$\kappa \colon [a,b] \to \mathbb {R}^{n-1}$$
κ
:
[
a
,
b
]
→

ℝ

n
−
1

of the curvature function of a plane curve. In the context of unit speed curves, this function $$\kappa $$
κ
determines $$\gamma $$
γ
up to an orientation-preserving rigid motion of $$\mathbb {R}^n$$

ℝ

n

. Before we can define $$\kappa $$
κ
, we have to study parallel normal vector fields along a curve in $$\mathbb {R}^n$$

ℝ

n

.
Curves in $$\mathbb {R}^3$$
Authors: Pinkall Ulrich , Gross Oliver 
Published: February 2024

AbstractFor a closed curve $$\gamma \colon [a,b]\to \mathbb {R}^3$$
γ
:
[
a
,
b
]
→

ℝ

3

with unit tangent field T, we can use a parallel normal vector field to transport a normal vector $$W_a\in T(a)^\perp $$

W

a

∈
T

(
a
)

⊥

at the starting point of $$\gamma $$
γ
to a normal vector $$W_b\in T(b)^\perp $$

W

b

∈
T

(
b
)

⊥

at the end point.
Curve shortening flow on Riemann surfaces with conical singularities
Authors: Roidos Nikolaos , Savas-Halilaj Andreas 
Published: February 2024

AbstractWe study the curve shortening flow on Riemann surfaces with finitely many conformal conical singularities. If the initial curve is passing through the singular points, then the evolution is governed by a degenerate quasilinear parabolic equation. In this case, we establish short time existence, uniqueness, and regularity of the flow. We also show that the evolving curves stay fixed at the singular points of the surface and obtain some contracting and convergence results.
IgG glycopeptide enrichment using hydrophilic interaction chromatography-based solid-phase extraction on an aminopropyl column
Authors: Molnarova Katarina , Chobotova Michaela , Kozlik Petr 
Published: February 2024

AbstractThe sample preparation step is pivotal in glycoproteomic analysis. An effective approach in glycoprotein sample preparation involves enriching glycopeptides by solid-phase extraction (SPE) using polar stationary phases in hydrophilic interaction liquid chromatography (HILIC) mode. The aim of this work is to show how different experimental conditions influence the enrichment efficiency of glycopeptides from human immunoglobulin G (IgG) on an aminopropyl-modified SPE column. Different compositions of the elution solvent (acetonitrile, methanol, and isopropanol), along with varying concentrations of elution solvent acidifiers (formic and acetic acid), and different concentrations of acetonitrile for the conditioning and washing solvents (65%, 75%, and 85% acetonitrile) were tested to observe their effects on the glycopeptide enrichment process. Isopropanol proved less effective in enriching glycopeptides, while acetonitrile was the most efficient, with methanol in between. Higher formic acid concentrations in the elution solvent weakened the ionic interactions, particularly with sialylated glycopeptides. Substituting formic acid with acetic acid led to earlier elution of more glycopeptides. The acetonitrile concentration in conditioning and washing solutions played a key role; at 65% acetonitrile, glycopeptides were not retained on the SPE column and were detected in the flow-through fraction. Ultimately, it was proven that the enrichment method was applicable to human plasma samples, resulting in a significant decrease in the abundances of non-glycosylated peptides. To the best of our knowledge, this study represents the first systematic investigation into the impact of the mobile phase on glycopeptide enrichment using an aminopropyl-modified SPE column in HILIC mode. This study demonstrates the substantial impact of even minor variations in experimental conditions, which have not yet been considered in the literature, on SPE-HILIC glycopeptide enrichment. Consequently, meticulous optimization of these conditions is imperative to enhance the specificity and selectivity of glycoproteomic analysis, ensuring accurate and reliable quantification.
Identification macrophage signatures in prostate cancer by single-cell sequencing and machine learning
Authors: Kang Zhen , Zhao Yu-Xuan , Qiu Ren Shun Qian , Chen Dong-Ning , Zheng Qing-Shui , Xue Xue-Yi , Xu Ning , Wei Yong 
Published: February 2024

Abstract
Background
The tumor microenvironment (TME) encompasses a variety of cells that influence immune responses and tumor growth, with tumor-associated macrophages (TAM) being a crucial component of the TME. TAM can guide prostate cancer in different directions in response to various external stimuli.

Methods
First, we downloaded prostate cancer single-cell sequencing data and second-generation sequencing data from multiple public databases. From these data, we identified characteristic genes associated with TAM clusters. We then employed machine learning techniques to select the most accurate TAM gene set and developed a TAM-related risk label for prostate cancer. We analyzed the tumor-relatedness of the TAM-related risk label and different risk groups within the population. Finally, we validated the accuracy of the prognostic label using single-cell sequencing data, qPCR, and WB assays, among other methods.

Results
In this study, the TAM_2 cell cluster has been identified as promoting the progression of prostate cancer, possibly representing M2 macrophages. The 9 TAM feature genes selected through ten machine learning methods and demonstrated their effectiveness in predicting the progression of prostate cancer patients. Additionally, we have linked these TAM feature genes to clinical pathological characteristics, allowing us to construct a nomogram. This nomogram provides clinical practitioners with a quantitative tool for assessing the prognosis of prostate cancer patients.

Conclusion
This study has analyzed the potential relationship between TAM and PCa and established a TAM-related prognostic model. It holds promise as a valuable tool for the management and treatment of PCa patients.
Sidedness is not a prognostic factor in an unselected cohort of patients with colon cancer but prognosis for caecal carcinoma is worse – A multivariate analysis of a large single institution database
Authors: Stelzner Sigmar , Mehdorn Matthias , Puffer Erik , Bleyl Dorothea , Kittner Thomas , Rhode Philipp , Gockel Ines , Mees Soeren T. 
Published: February 2024

Abstract
Purpose
Sidedness has emerged as a prognostic factor for metastatic colorectal cancer treated with modern systemic therapies. This study investigates whether it is also relevant for an unselected patient cohort including all stages.

Methods
All consecutive patients admitted with colon cancer between 1995 and 2018 were retrieved from an institution-held database. Patients were divided into two cohorts. The first cohort included patients without distant metastases who were able to undergo curative resection. The second cohort presented with distant metastases (stage IV). Potentially prognostic factors were subjected to multivariate Cox Regression analysis.

Results
Overall, 1,606 patients met the inclusion and exclusion criteria. An R0-resection was achieved in 1,222 patients without distant metastases. Five-year cause-specific survival rate was 89.3% for this group. There was no difference between right- and left-sided cancers (88.2% vs. 90.1%, p = 0.220). However, prognosis of caecal carcinoma was significantly worse than that of all other sites combined (83.5% vs. 90.2%, p = 0.007). In multivariate analysis, pT-category, pN-category, grading, vascular invasion, emergency operation, adjuvant chemotherapy, and caecal carcinoma remained as independent prognostic factors. In the 384 patients with stage IV-disease, 3-year overall survival for right- vs. left-sided cancers differed only in univariate analysis (17.7% vs. 28.6%, p = 0.013).

Conclusion
In non-metastatic colon cancer, location in the caecum is an independent prognostic factor. In unselected patients with stage IV colon cancer, sidedness was not found to be a prognostic factor. Differentiation into right- and left-sided tumors may be simplistic, and further studies on the biological behavior of different colonic sites are warranted.
Interplay of the Mediterranean diet and genetic hypertension risk on blood pressure in European adolescents: Findings from the HELENA study
Authors: Pérez-Gimeno Gloria , Seral-Cortes Miguel , Sabroso-Lasa Sergio , Esteban Luis Mariano , Widhalm Kurt , Gottrand Frederic , Stehle Peter , Meirhaeghe Aline , Muntaner Manon , Kafatos Anthony , Gutierrez Angel , Manios Yannis , Anastasiou Costas A. , Gonzalez-Gross Marcela , Breidenassel Christina , Censi Laura , de Henauw Stefaan , Labayen Idoia , Bueno-Lozano Gloria , Rupérez Azahara I. , Moreno Luis A. 
Published: February 2024

AbstractEarly-life onset of high blood pressure is associated with the development of cardiovascular diseases in adulthood. In adolescents, limited evidence exists regarding the association between adherence to the Mediterranean Diet (MedDiet) and normal blood pressure (BP) levels, as well as its potential to modulate genetic predisposition to HTN. This study investigated the interaction between a MedDiet score and a recently developed HTN-genetic risk score (HTN-GRS) on blood pressure levels in a European adolescent cohort. The MedDiet score was derived from two non-consecutive 24-h dietary recalls and ranged from 0 (indicating low adherence) to 9 (indicating high adherence). Multiple linear regression models, adjusted for covariates, were employed to examine the relationship between the MedDiet score and BP z-scores and to assess the interaction effects between the MedDiet score and HTN-GRS on BP z-scores. MedDiet score showed a negative association with z-systolic BP (SBP) (ß = −0.40, p < 0.001) and z-diastolic BP (DBP) (ß = −0.29, p = 0.001). Additionally, a significant interaction effect was identified between the MedDiet score and HTN-GRS on z-SBP (ß = 0.02, p < 0.001) and z-DBP (ß = 0.02, p < 0.001). The modulatory effect of the MedDiet was more pronounced in females than in males, and HTN-GRS exhibited a stronger influence on DBP than on SBP. Conclusion: The study suggests that higher adherence to the MedDiet is associated with reduced BP levels in adolescents and provides evidence of a genetic-diet interaction influencing BP in adolescents.

What is Known:• Adherence to the Mediterranean diet may reduce BP levels.

What is New:• It is the first study to assess the connection between adherence to a Mediterranean diet, a hypertension genetic risk score, and how they interact in influencing blood pressure.• It is conducted within a multicenter cohort of European adolescents.
Mitochondrial genetic variation and risk of chronic kidney disease and acute kidney injury in UK Biobank participants
Authors: Jotwani Vasantha , Yang Stephanie Y. , Thiessen-Philbrook Heather , Parikh Chirag R. , Katz Ronit , Tranah Gregory J. , Ix Joachim H. , Cummings Steve , Waikar Sushrut S. , Shlipak Michael G. , Sarnak Mark J. , Parikh Samir M. , Arking Dan E. 
Published: February 2024

AbstractExperimental models suggest an important role for mitochondrial dysfunction in the pathogenesis of chronic kidney disease (CKD) and acute kidney injury (AKI), but little is known regarding the impact of common mitochondrial genetic variation on kidney health. We sought to evaluate associations of inherited mitochondrial DNA (mtDNA) variation with risk of CKD and AKI in a large population-based cohort. We categorized UK Biobank participants who self-identified as white into eight distinct mtDNA haplotypes, which were previously identified based on their associations with phenotypes associated with mitochondrial DNA copy number, a measure of mitochondrial function. We used linear and logistic regression models to evaluate associations of these mtDNA haplotypes with estimated glomerular filtration rate by serum creatinine and cystatin C (eGFRCr-CysC, N = 362,802), prevalent (N = 416 cases) and incident (N = 405 cases) end-stage kidney disease (ESKD), AKI defined by diagnostic codes (N = 14,170 cases), and urine albumin/creatinine ratio (ACR, N = 114,662). The mean age was 57 ± 8 years and the mean eGFR was 90 ± 14 ml/min/1.73 m2. MtDNA haplotype was significantly associated with eGFR (p = 2.8E−12), but not with prevalent ESKD (p = 5.9E−2), incident ESKD (p = 0.93), AKI (p = 0.26), or urine ACR (p = 0.54). The association of mtDNA haplotype with eGFR remained significant after adjustment for diabetes mellitus and hypertension (p = 1.2E−10). When compared to the reference haplotype, mtDNA haplotypes I (β = 0.402, standard error (SE) = 0.111; p = 2.7E−4), IV (β = 0.430, SE = 0.073; p = 4.2E−9), and V (β = 0.233, SE = 0.050; p = 2.7E−6) were each associated with higher eGFR. Among self-identified white UK Biobank participants, mtDNA haplotype was associated with eGFR, but not with ESKD, AKI or albuminuria.
Ein Instrument zur Erfassung biopsychosozialer Schmerzkonzepte von Erwachsenen
Authors: Wickering L. , Lautwein C. , Fiegler A. , Allerdißen L. , Kloos T. , Schneider M. , Hechler T. 
Published: February 2024

Zusammenfassung
Hintergrund
Das biopsychosoziale Modell ist Grundlage für das Verständnis und die Behandlung chronischer Schmerzen. Ob Betroffene ein biopsychosoziales Verständnis zeigen, ist wenig erforscht. Hier wird der multidimensionale Fragebogen „Biopsychosoziale Schmerzkonzept Matrix“ (BiPS Matrix) vorgestellt. Die Konzeption der BiPS Matrix basiert sowohl auf den Bereichen biologisch, psychologisch und sozial als auch auf dem Common-Sense Model of Self-Regulation mit fünf Dimensionen: (1) Art der Störung, (2) Annahmen zur Ursache, (3) Konsequenzen, (4) zeitlicher Krankheitsverlauf, (5) Möglichkeiten der Kontrolle/Behandlung.

Ziel
Ziel der vorliegenden Studie ist die Erfassung der inhaltlichen Relevanz und Verständlichkeit der Bereiche, Dimensionen und Items inklusive der Verwendung der BiPS Matrix mit Kindern durch interdisziplinäre Expert*innen-Ratings. Perspektivisch kann der Fragebogen von Behandelnden im Rahmen der Diagnostik angewendet werden.

Methode
In einer Online-Studie wurden 17 Expert*innen befragt. Neben deskriptiven Statistiken wurden Kommentare mittels qualitativer Inhaltsanalyse nach Mayring ausgewertet.

Ergebnisse
Alle Expert*innen schätzten die Erfassung von Schmerzkonzepten mit der BiPS Matrix sowie die Bereiche und Dimensionen als sehr relevant ein. Hinsichtlich der Items wurden vorwiegend Vorschläge bezüglich der Itemformulierungen sowie Anpassungsvorschläge für Kinder gemacht.

Diskussion
Die BiPS Matrix stellt aus Expert*innensicht ein relevantes Instrument dar. Weitere Forschung zur psychometrischen Überprüfung der BiPS Matrix bei Erwachsenen und Kindern ist indiziert. Daneben kann die BiPS Matrix auch zur Erforschung von Schmerzkonzepten an medizinischen und psychotherapeutischen Berufsgruppen zur Abbildung des biopsychosozialen Schmerzverständnisses und der damit einhergehenden Behandlungsangebote eingesetzt werden.
Exploring emergent syllables in end-to-end automatic speech recognizers through model explainability technique
Authors: Vitale Vincenzo Norman , Cutugno Francesco , Origlia Antonio , Coro Gianpaolo 
Published: February 2024

AbstractAutomatic speech recognition systems based on end-to-end models (E2E-ASRs) can achieve comparable performance to conventional ASR systems while reproducing all their essential parts automatically, from speech units to the language model. However, they hide the underlying perceptual processes modelled, if any, and they have lower adaptability to multiple application contexts, and, furthermore, they require powerful hardware and an extensive amount of training data. Model-explainability techniques can explore the internal dynamics of these ASR systems and possibly understand and explain the processes conducting to their decisions and outputs. Understanding these processes can help enhance ASR performance and reduce the required training data and hardware significantly. In this paper, we probe the internal dynamics of three E2E-ASRs pre-trained for English by building an acoustic-syllable boundary detector for Italian and Spanish based on the E2E-ASRs’ internal encoding layer outputs. We demonstrate that the shallower E2E-ASR layers spontaneously form a rhythmic component correlated with prominent syllables, central in human speech processing. This finding highlights a parallel between the analysed E2E-ASRs and human speech recognition. Our results contribute to the body of knowledge by providing a human-explainable insight into behaviours encoded in popular E2E-ASR systems.
Impact of the novel coronavirus infection on pediatric surgery: an analysis of data from the National Clinical Database
Authors: Ise Kazuya , Tachimori Hisateru , Fujishiro Jun , Tomita Hirofumi , Suzuki Kan , Yamamoto Hiroyuki , Miyata Hiroaki , Fuchimoto Yasushi 
Published: February 2024

Abstract
Purpose
The coronavirus disease 2019 (COVID-19) pandemic limited the delivery of medical resources. Although surgeries are triaged according to disease severity and urgency, a delay in diagnosis and surgery can be detrimental. We conducted this study to analyze data on the impact of the COVID-19 pandemic on pediatric surgery for different diseases or disorders.

Methods
We compiled and compared data on pediatric surgical cases from 2018 to 2020, using the National Clinical Database. The number of diseases, severity, complication rates, mortality rates by disease/disorder, and the COVID-19 pandemic areas were analyzed.

Results
The total number of cases of pediatric surgery in 2018, 2019, and 2020 was 50,026, 49,794, and 45,621, respectively, reflecting an 8.8% decrease in 2020 from 2018 and an 8.4% decrease in 2020 from 2019. A decrease was observed when the number of patients with COVID-19 was high and was greater in areas with a low infection rate. There was a marked decrease in the number of inguinal hernia cases. The number of emergency room visits and emergency surgeries decreased, but their relative proportions increased.

Conclusions
The COVID-19 pandemic decreased the number of pediatric surgeries, reflecting the limitations of scheduled surgeries and infection control measures.
A novel lncRNA-hidden polypeptide regulates malignant phenotypes and pemetrexed sensitivity in A549 pulmonary adenocarcinoma cells
Authors: Han Xiaobing , Chen Liangxin , Sun Peng , Wang Xiuqing , Zhao Qian , Liao Lingfeng , Lou Dejin , Zhou Nan , Wang Yujun 
Published: February 2024

AbstractThe advance of high-throughput sequencing enhances the discovery of short ORFs embedded in long non-coding RNAs (lncRNAs). Here, we uncovered the production and biological activity of lncRNA-hidden polypeptides in lung adenocarcinoma (LUAD). In the present study, bioinformatics was used to screen the lncRNA-hidden polypeptides in LUAD. Analysis of protein expression was done by western blot or immunofluorescence assay. The functions of the polypeptide were determined by detecting its effects on cell viability, proliferation, migration, invasion, and pemetrexed (PEM) sensitivity. The protein interactors of the polypeptide were analyzed by mass spectrometry after Co-immunoprecipitation (Co-IP) assay. The results showed that the lncRNA LINC00954 was confirmed to encode a novel polypeptide LINC00954-ORF. The polypeptide had tumor-suppressor features in A549 cells by repressing cell growth, motility and invasion. Moreover, the polypeptide enhanced PEM sensitivity and suppressed growth in A549/PEM cells. The protein interactors of this polypeptide had close correlations with RNA processing, amide metabolic process, translation, RNA binding, RNA transport, and DNA replication. As a conclusion, the LINC00954-ORF polypeptide embedded in lncRNA LINC00954 possesses tumor-suppressor features in A549 and PEM-resistant A549 cells and sensitizes PEM-resistant A549 cells to PEM, providing evidence that the LINC00954-ORF polypeptide is a potential anti-cancer agent in LUAD.
Unexpected findings: loss of corneal endothelial cells in Uygur patients with exfoliation syndrome
Authors: Ma Yinu , Li Qin , Dong Yue , Yi Xianglong 
Published: February 2024

Abstract
Purpose
This study aimed to investigate anterior segment parameters in patients with exfoliation syndrome (XFS) and exfoliation glaucoma (XFG).

Methods
The study adopted a retrospective case series design, involving a total of 56 patients (112 eyes) with unrelated XFS/XFG (XFS: 26 patients/60 eyes; XFG: 30 patients/44 eyes) and 100 age-related cataract cases as the control group (200 eyes). The participants were evaluated at the ophthalmology department of the First Affiliated Hospital of Xinjiang Medical University. Clinical data, including eye axial length, anterior chamber depth, white-to-white distance, central corneal thickness, and corneal endothelial cell density (ECD), were collected for statistical analysis.

Results
ECD exhibited a significant difference between the XFS/XFG and age-related cataract groups (P < 0.001), while the remaining indexes did not show statistical differences (P > 0.05). Ocular parameters in patients with XFS and XFG were distinct from those in age-related cataract cases, with consistent results. Notably, there were no statistically significant differences between XFS and XFG patients.

Conclusions
ECD is reduced in XFS/XFG patients compared with age-related cataract subjects. It is crucial to remain vigilant to enhance surgical safety in XFS/XFG patients and prevent complications proactively.