bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive Model for Outcomes in Inflammatory Bowel Disease Patients Receiving Maintenance Infliximab Therapy
Authors: Wong Rochelle , Charilaou Paris , Hemperly Amy , Qin Lihui , Pan Yushan , Mathani Prerna , Longman Randy , Boland Brigid S , Dulai Parambir S , Holmer Ariela K , Lukin Dana , Singh Siddharth , Valasek Mark A , Sandborn William J , Scherl Ellen , Vande Casteele Niels , Battat Robert 
Published: November 2024

Abstract

Background
No models predict future outcomes in inflammatory bowel disease (IBD) patients receiving maintenance infliximab therapy. We created a predictive model for unfavorable outcomes.

Methods
Adult patients with IBD receiving maintenance infliximab therapy at 2 centers with matched serum infliximab concentrations and blinded histologic scores (Robarts Histopathologic Index [RHI]) were included. The primary endpoint was an unfavorable outcome of active objective inflammation or need for IBD-related surgery or hospitalization at 6–18 months follow-up. Internal variables were identified using univariable analyses, modeling used multivariable analysis, and performance was assessed (area under receiver-operating curve [AUC]) and externally validated.

Results
In 81 patients, 40.7% developed unfavorable outcomes at follow-up. Infliximab concentration &lt;9.3 µg/mL (odds ratio [OR] 5.3, P = .001) and RHI &gt; 12 (OR 3.4, P = .03) were the only factors associated with developing the primary unfavorable outcome. A prediction score assigning 1 point to each variable had good discrimination and performed similarly on internal (AUC 0.71) and external (AUC 0.73) cohorts. The risk of primary unfavorable outcomes in internal and external cohorts, respectively, was 23% and 15% for a score of 0, 46% and 50% for a score of 1, and 100% and 75% for a score of 2. Infliximab concentration alone performed similar to the 2-predictor model in internal (AUC 0.65, P = .5 vs. 2-predictor model) and external (AUC 0.70, P = .9, vs. 2-predictor model) cohorts.

Conclusions
Using unbiased variable selection, a 2-predictor model using infliximab concentrations and histology identified IBD patients on maintenance infliximab therapy at high risk of future unfavorable outcomes. For practical applicability, infliximab concentrations alone performed similarly well.
Accuracy of left ventricular mechanical dyssynchrony indices for mechanical characteristics of left bundle branch block using cardiovascular magnetic resonance feature tracking
Authors: Loewenstein Daniel E , Wieslander Björn , Heiberg Einar , Axelsson Jimmy , Klem Igor , Nijveldt Robin , Schelbert Erik B , Sörensson Peder , Sigfridsson Andreas , Strauss David G , Kim Raymond J , Atwater Brett D , Ugander Martin 
Published: November 2024

Abstract

Aims
More than 90% of patients with left bundle branch block (LBBB) and reduced left ventricular (LV) ejection fraction have LV dyssynchrony and a high probability of response to cardiac resynchronization therapy (CRT). A subgroup of patients with non-specific intraventricular conduction delay (IVCD) have a LBBB-like LV activation pattern when studied using invasive mapping and advanced echocardiographic techniques. These patients also frequently benefit from CRT, but these patients have proven difficult to identify using electrocardiogram criteria. Cardiovascular magnetic resonance (CMR) imaging indices of dyssynchrony may identify patients with IVCD who may benefit from CRT, but their relative accuracies for identification of LV dyssynchrony remain unknown. We compared the LV dyssynchrony classification accuracy of two commonly available CMR indices in a study population of patients with severely reduced LV ejection fraction and no scar and either LBBB or QRS duration &lt;120 ms and normal QRS axis (controls).

Methods and results
In LBBB (n = 44) and controls (n = 36), using CMR feature-tracking circumferential strain, dyssynchrony was quantified as the circumferential uniformity ratio estimate (CURE) and the systolic stretch index (SSI). Deidentified CMR image data were made publicly available. Both CURE and SSI quantified more severe dyssynchrony in LBBB compared with controls (P&lt;0.001 for both). SSI more frequently discriminated LBBB and normal conduction LV activation patterns than CURE [area under the receiver-operating characteristic curve (95% confidence interval) 0.96 (0.92–1.00) for SSI vs. 0.76 (0.65–0.86) for CURE, P &lt; 0.001].

Conclusion
SSI is superior to CURE for discriminating synchronous and dyssynchronous LV activation and should be further studied in the setting of non-LBBB conduction abnormalities.
PIEZO1 attenuates Marfan syndrome aneurysm development through TGF-β signaling pathway inhibition via TGFBR2
Authors: Yang Peiwen , Liu Hao , Wang Shilin , Xiao Xiaoyue , Jiang Lang , Le Sheng , Chen Shanshan , Ye Ping , Xia Jiahong 
Published: November 2024

Abstract

Background and Aims
Marfan syndrome (MFS) is a hereditary disorder primarily caused by mutations in the FBN1 gene. Its critical cardiovascular manifestation is thoracic aortic aneurysm (TAA), which poses life-threatening risks. Owing to the lack of effective pharmacological therapies, surgical intervention continues to be the current definitive treatment. In this study, the role of Piezo-type mechanosensitive ion channel component 1 (Piezo1) in MFS was investigated and the activation of PIEZO1 was identified as a potential treatment for MFS.

Methods
PIEZO1 expression was detected in MFS mice (Fbn1C1041G/+) and patients. Piezo1 conditional knockout mice in vascular smooth muscle cells of MFS mice (MFS × CKO) was generated, and bioinformatics analysis and experiments in vitro and in vivo were performed to investigate the role of Piezo1 in MFS.

Results
PIEZO1 expression decreased in the aortas of MFS mice; MFS × CKO mice showed aggravated TAA, inflammation, extracellular matrix remodelling, and TGF-β pathway activation compared to MFS mice. Mechanistically, PIEZO1 knockout exacerbated the activation of the TGF-β signalling pathway by inhibiting the endocytosis and autophagy of TGF-β receptor 2 mediated by Rab GTPase 3C. Additionally, the pharmacological activation PIEZO1 through Yoda1 prevented TGF-β signalling pathway activation and reversed TAA in MFS mice.

Conclusions
Piezo1 deficiency aggravates MFS aneurysms by promoting TGF-β signalling pathway activation via TGF-β receptor 2 endocytosis and a decrease in autophagy. These data suggest that PIEZO1 may be a potential therapeutic target for MFS treatment.
Determination of 28 food safety risk factors in novel foods by ultra-high performance liquid chromatography-quadrupole/orbitrap high resolution mass spectrometry
Authors: Fan Sufang , Ren Xiaowei , Shi Guohua , Zhao Limin , Ma Junmei , Wen Di , Li Qiang , Zhang Yan 
Published: November 2024

Abstract
An analytical method was established for the determination of 24 food safety risk factors (18 heterocyclic aromatic amines, 6 mycotoxins) in synthetic meat and synthetic protein samples, 4 microcystins in microalgae samples using ultra-high performance liquid chromatography-quadrupole/orbitrap high resolution mass spectrometry (UPLC-Q/Orbitrap HRMS). The novel synthetic food was extracted using a 50% methanol solution and purified with 3 mL of n-hexane saturated with a 50% methanol solution. For microalgae samples, extraction was performed with an 80% acetonitrile solution and purified using a PRiME HLB solid-phase extraction column. An ACQUITY HSS T3 column (100 mm ×2.1mm, 1.8 μm) was used for analyte separation, with 5 mmol/L ammonium acetate containing 0.01% formic acid and methanol selected as the mobile phase. Gradient elution was adopt. Data acquisition was conducted in both positive and negative mode using full scan-data dependent secondary scan mode (Full MS-ddMS2). Matrix-matched standards were employed for quantification in the external standard method. Additionally, mzVault and Tracefinder software were used to establish a screening database for 28 food safety risk factors. The results showed that the relative deviation of the exact mass of the 28 food safety risk factors was less than 5ppm, with good linearity in the range of 1-100μg/kg, and a correlation coefficient (r2) of ≥0.9978. The detection limit ranged from 0.5 to 4 μg/kg, and the quantification limit ranged from 1 to 10 μg/kg. Method recoveries ranged from 70.0% to 119.6% with relative standard deviations of 0.4% to 14.6% (n=6). The method is simple, sensitive and accurate, suitable for rapid screening of 28 food safety risk factors in novel foods.
Effects of cashew nutshell extract inclusion into a high-grain finishing diet on methane emissions, nutrient digestibility, and ruminal fermentation in beef steers
Authors: Cuervo Wilmer , Gomez Camila , Tarnonsky Federico , Fernandez-Marenchino Ignacio , Podversich Federico , Maderal Araceli , Schulmeister Tessa M , Vargas Juan de J , DiLorenzo Nicolas 
Published: November 2024

Abstract
By 2050, the U.S. beef industry must produce an extra 40 million tons of beef to satisfy the global demand. Such an increase in inventory will undoubtedly enhance methane (CH4) production from livestock, which should be reduced by over 20%. The addition of plant secondary metabolites, such as anacardic acid present in cashew nutshell extract (CNSE), has shown promising results in reducing CH4 yield, although its effects seemed to be diet-dependent. This study evaluated the addition of CNSE to a high-grain diet (85:15 grain:forage) on in vivo CH4 emissions, nutrient digestibility, performance, feeding behavior, and ruminal fermentation parameters of beef steers. Sixteen Angus crossbred steers [599 ± 40 kg of bodyweight (BW)] and 6 ruminally cannulated crossbred steers (490 ± 51 kg of BW) were utilized in a crossover design with 2 experimental periods of 56 d each, composed by 14 d of adaptation, 35 d of measurement, and 7 d of washout. Following adaptation, steers were sorted by BW, and assigned to receive no additive (CON) or CNSE at 5 g/steer/d. Data were analyzed using the MIXED procedure of SAS. Inclusion of CNSE increased (P &lt; 0.05) propionate concentration and molar proportion (MP; mol/100 mol), tended to decrease acetate MP (P = 0.10), reduced the acetate:propionate (A:P) ratio (P = 0.05), and MP of branched-chain volatile fatty acids (P &lt; 0.01). Neither in vitro organic matter digestibility nor in vitro CH4 yield were affected by CNSE inclusion (P &gt; 0.05). Steers receiving CNSE exhibited greater (P &lt; 0.05) final BW, dry matter intake (DMI), and average daily gain (ADG) but lesser (P &lt; 0.05) in vivo CH4 emission rate (g/d), yield (g/kg of DMI), and intensity (g/kg of ADG). Meal length, bunk visit duration, and apparent total tract digestibility of DM increased (P &lt; 0.05) after CNSE addition. Considering CNSE-supplemented steers spent more time in the feedbunk and exhibited higher DMI, CH4 mitigation was unlikely associated with intake reduction. The addition of CNSE to a high-grain diet in beef steers demonstrated significant improvements in animal performance and reduced CH4 emissions, as the result of shifts in ruminal fermentation patterns, favoring propionate instead of acetate concentration, leading to a reduction in the A:P ratio. CNSE shows promise as a strategy to enhance beef industry sustainability.
Course and treatment of severe osteoporosis complicated by calciphylaxis: a case report
Authors: Tominaga Ayako , Wada Keiji , Kato Yoshiharu , Okazaki Ken 
Published: November 2024

Abstract
Calciphylaxis, also known as calcific uremic arteriolopathy (CUA), is a rare disorder with many unknown treatment and diagnostic aspects. It is characterized by calcification and thrombosis of small blood vessels. This disease leads to progressive skin calcification, necrotizing ulcers, and infections and is associated with a high mortality rate. Although primarily affected sites tend to be on skin, those affecting bones are also significant. We report a case of CUA complicated with rapidly progressing multiple vertebral fractures and severe osteoporosis. The patient experienced a series of five vertebral fractures within 5 months after hospitalization, and blood tests revealed abnormally high levels of bone resorption marker bone-type tartrate-resistant acid phosphatase (TRACP-5b). Consequently, intravenous sodium thiosulfate and hyperbaric oxygen therapy were administered for the treatment of skin lesions caused by calciphylaxis, and brace therapy and denosumab treatment were initiated for vertebral fractures. This approach rapidly decreased TRACP-5b levels and arrested the chain of vertebral fractures. We concluded that to maintain the quality of life of patients with CUA, early treatment of primary skin lesions as well as comorbid conditions is essential.
A Rat’s Progress: Plague and the “Migratory Rat” in British India, 1896-1899
Authors: Lynteris Christos 
Published: November 2024

Abstract
Whether referring to oceanic travel on board of ships or to movement in terra firma, framings of the “migratory rat” formed a key epidemiological component of approaches to the Third Plague Pandemic (1894-1959) as the first pandemic to be understood as caused by a zoonotic disease. In this article, I examine the emergence and development of scientific framings of the migratory rat in the first, explosive years of the third plague pandemic in India (1896-1899). Examining publications and archival sources, I ask how this animal figure came to inform and transform epidemiological reasoning. Going beyond established approaches that have shown how the rat-plague relation was mobilised by colonial doctors to pathologise Indigenous lifeways, I argue that more complex and ambivalent processes were also set in motion by this figure. First, I show how the migratory rat became invested with attributes of invasiveness that assumed ontological qualities in colonial epidemiological reasoning. Second, comparing the migratory rat with the hitherto established “staggering rat,” I argue that the former embodied new approaches to both space and time in epidemiology. Third, I show how Indigenous scientists came to mobilise this complex figure to contest colonial approaches to plague.
Association of race and area of deprivation index with prostate cancer incidence and lethality: results from a contemporary North American cohort
Authors: Finati Marco , Stephens Alex , Cirulli Giuseppe Ottone , Chiarelli Giuseppe , Tinsley Shane , Morrison Chase , Sood Akshay , Buffi Nicolò , Lughezzani Giovanni , Salonia Andrea , Briganti Alberto , Montorsi Francesco , Busetto Gian Maria , Rogers Craig , Carrieri Giuseppe , Abdollah Firas 
Published: November 2024

Abstract

Background
Socioeconomic and demographic factors contribute to disparity in prostate cancer (PCa) outcomes. We examined the impact of Area of Deprivation Index (ADI) and race on PCa incidence and lethality in a North American cohort.

Methods
Our cohort included men who received at least 1 prostate-Specifig Antigen (pSA) test within our Health System (1995-2022). An ADI score was assigned to each patient based on their residential census block, ranked as a percentile of deprivation relative to the national level. Individuals were further categorized into quartiles, where the fourth one (ADI 75-100) represented those living in the most deprived areas. We investigated PCa incidence and lethality, using cumulative incidence estimates and competing-risk regression. An ADI × Race interaction term examined whether the relationship between ADI and outcomes varied based on race.

Results
We included 134 366 patients, 25% of whom were non-Hispanic Black (NHB). Median (IQR) follow-up was 8.8 (5-17) years. At multivariate analysis, individuals from the third quartile (ADI 50-74, 95% CI = 0.83 to 0.95) and the fourth quartile (ADI ≥75, 95% CI = 0.75 to 0.86) showed significant reduced hazard ratios for PCa incidence, when compared with the first quartile (ADI &lt;25, all P &lt; .001). In contrast to the overall cohort, PCa incidence increased with ADI in NHB men, who were persistently at higher hazard for both PCa incidence and lethality than non-Hispanic White (NHW), across all ADI strata (all P &lt; .001).

Conclusions
Living in more deprived areas was associated with lower PCa incidence and higher lethal disease rate. Conversely, PCa incidence increased with ADI for NHB, who consistently showed worse outcomes than NHW individuals, regardless of ADI.
Defects and waves in anisotropic and layered media: Stroh formalism in terms of the Cartesian system of vector functions
Authors: Qu Yilin , Zhu Feng , Pan Ernian 
Published: November 2024

ABSTRACT
When waves propagate through anisotropic elastic media, P- and SV-type waves (Rayleigh waves) are generally coupled with SH-type waves (Love waves). In contrast, in isotropic elastic media, SH/Love waves are decoupled and separate from other body/surface waves. However, the conditions under which these waves in anisotropic media may be decoupled remain unclear. In this paper, we introduce a Cartesian vector function system, named as the Cartesian LMN vector system, and derive solutions using this system within the Stroh formalism. This approach inherently accounts for both coupling and decoupling cases. Various source functions based on the Cartesian LMN vector system are derived. The Cartesian LMN system further enables a straightforward reduction to two-dimensional wave problems, including simplified source functions for line forces and lattice dislocations.
Renewable energy and energy justice in the Middle East: international human rights, environmental and climate change law and policy perspectives
Authors: Maniruzzaman A F M , Al-Saleem Khalid 
Published: November 2024

Abstract
The concept of energy justice is now a divisive issue throughout the world. Clean energy is becoming increasingly unavailable to a large portion of the population. Against this backdrop, this article explores the legal aspects of renewable energy and energy justice in three major, traditionally energy-rich countries representing the Middle East: the Kingdom of Saudi Arabia (KSA), Iran, and Iraq. It critically evaluates these countries’ legal challenges of renewable energy and energy justice. The research found that renewable energy is becoming more necessary for sustainable development and resilience to climate change. Natural resource abundance, increasing energy use, and a commitment to global climate change goals all pose unique challenges and opportunities for countries in the Middle East region. From international human rights, environmental, and climate change law perspectives, this article analyses the current regulatory processes and legislative frameworks aimed at increasing the use of renewable energy sources and ensuring energy justice. Renewable energy in the Middle East has been influenced by regional initiatives, international treaties, and national legislation, all of which are examined in detail.
icecube AGN neutrino candidate PKS 1717+177: dark deflector bends nuclear jet
Authors: Britzen S , Kovačević A B , Zajaček M , Popović L Č , Pashchenko I N , Kun E , Pánis R , Jaron F , Plšek T , Tursunov A , Stuchlík Z 
Published: November 2024

ABSTRACT
The BL Lac object PKS 1717+177 has been identified as potential neutrino-emitting active galactic nuclei in the point source stacking analysis of icecube data. We explore peculiarities in the morphology and kinematics of the jet and examine multiwavelength light curves for distinctive effects which might allow to pinpoint a likely neutrino generation mechanism. We re-modelled 34 high-resolution radio interferometric Very Long Baseline Array observations obtained at 15 GHz (between 1999 December 27 and 2023 May 3). A correlation and periodicity analysis of optical Katzman Automatic Imaging Telescope and Tuorla data, as well as for Fermi-LAT $\gamma$-ray data has been performed. The nuclear jet appears deflected and bent at about 0.5 mas distance from the radio core by an encounter with a dark, unseen object. The deviation of the jet evolves over 23.5 yr from a simple apparent bend into a significantly meandering structure with increasing amplitude: a zig-zag line. To our knowledge, this is the first time that the temporal evolution of a jet deviation can be traced. The turning point shifts with time and the jet seems to brighten up almost periodically at the point of deviation. The radio core as well as the jet contribute approximately equally to the total flux-density at 15 GHz. We discuss scenarios which could explain the complex jet bending and quasi-regular flaring. We propose that the jet could either be deflected by the magnetosphere of a second massive black hole, by the pressure gradient due to a circumnuclear dense cloud, or via gravitational lensing by an intervening black hole.
TPCNet: representation learning for H i mapping
Authors: Nguyen Hiep , Tang Haiyang , Alger Matthew , Marchal Antoine , Muller Eric G M , Ong Cheng Soon , McClure-Griffiths N M 
Published: November 2024

ABSTRACT
We introduce TPCNet, a neural network predictor that combines convolutional and transformer architectures with positional encodings, for neutral atomic hydrogen (H i) spectral analysis. Trained on synthetic data sets, our models predict cold neutral gas fraction ($f_\mathrm{CNM}$) and H i opacity correction factor ($\mathcal {R_{\mathrm{H\,{\small I}}}}$) from emission spectra based on the learned relationships between the desired output parameters and observables (optically thin column density and peak brightness). As a follow-up to Murray et al.’s shallow Convolutional Neural Network (CNN), we construct deep CNN models and compare them to TPCNet models. TPCNet outperforms deep CNNs, achieving a 10 per cent average increase in testing accuracy, algorithmic (training) stability, and convergence speed. Our findings highlight the robustness of the proposed model with sinusoidal positional encoding applied directly to the spectral input, addressing perturbations in training data set shuffling and convolutional network weight initializations. Higher spectral resolutions with increased spectral channels offer advantages, albeit with increased training time. Diverse synthetic data sets enhance model performance and generalization, as demonstrated by producing $f_\mathrm{CNM}$ and $\mathcal {R_{\mathrm{H\,{\small I}}}}$ values consistent with evaluation ground truths. Applications of TPCNet to observed emission data reveal strong agreement between the predictions and Gaussian decomposition-based estimates (from emission and absorption surveys), emphasizing its potential in H i spectral analysis.