bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes
Authors: Sperling Alexis L. , Eves-van den Akker Sebastian 
Published: December 2023

Abstract
Background
Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant.

Results
We present the Sperling prep - a whole mount method for nematode preparation that enables staining with small molecules, antibodies, or in situ hybridization chain reaction. This method does not require specialized apparatus and utilizes typical laboratory equipment and materials. By dissociating the strong cuticle and interior muscle layers, we enabled entry of the small molecule stains into the tissue. After permeabilization, small molecule stains can be used to visualize the nuclei with the DNA stain DAPI and the internal structures of the digestive tract and longitudinal musculature with the filamentous actin stain phalloidin. The permeabilization even allows entry of larger antibodies, albeit with lower efficiency. Finally, this method works exceptionally well with in situ HCR. Using this method, we have visualized effector transcripts specific to the dorsal gland and the subventral grand of the sugar beet cyst nematode, Heterodera schachtii, multiplexed in the same nematode.

Conclusion
We were able to visualize the internal structures of the nematode as well as key effector transcripts that are used during plant infection and parasitism. Therefore, this method provides an important toolkit for studying the biology of plant-parasitic nematodes.
Iron as an emerging therapeutic target in critically ill patients
Authors: Grange Coralie , Lux François , Brichart Thomas , David Laurent , Couturier Aymeric , Leaf David E. , Allaouchiche Bernard , Tillement Olivier 
Published: December 2023

AbstractThe multiple roles of iron in the body have been known for decades, particularly its involvement in iron overload diseases such as hemochromatosis. More recently, compelling evidence has emerged regarding the critical role of non-transferrin bound iron (NTBI), also known as catalytic iron, in the care of critically ill patients in intensive care units (ICUs). These trace amounts of iron constitute a small percentage of the serum iron, yet they are heavily implicated in the exacerbation of diseases, primarily by catalyzing the formation of reactive oxygen species, which promote oxidative stress. Additionally, catalytic iron activates macrophages and facilitates the growth of pathogens. This review aims to shed light on this underappreciated phenomenon and explore the various common sources of NTBI in ICU patients, which lead to transient iron dysregulation during acute phases of disease. Iron serves as the linchpin of a vicious cycle in many ICU pathologies that are often multifactorial. The clinical evidence showing its detrimental impact on patient outcomes will be outlined in the major ICU pathologies. Finally, different therapeutic strategies will be reviewed, including the targeting of proteins involved in iron metabolism, conventional chelation therapy, and the combination of renal replacement therapy with chelation therapy.
Nutritional knowledge, attitude, and practice of professional athletes in an Iranian population (a cross-sectional study)
Authors: Hasanpouri Amin , Rahmani Bita , Gharakhanlou Bahram Jamali , Solaimanian Shahabaddin , Shahsavari Saeed , Rasouli Ahmadreza , Abbasi Saeed , Ebrahimi-Kalan Abbas , Rouzitalab Tohid , Hoseinabadi Zahra , Shiri-Shahsavar Mohammad Reza 
Published: December 2023

Abstract
Background
Proper nutrition is vital in promoting community health, yet insufficient knowledge and improper dietary practices can lead to deficiencies and diseases. Professional athletes depend on optimal nutrition for their performance and recovery, but a lack of understanding can impede their potential. The nutritional status of athletes impacts their overall health and sports performance. Inadequate sports nutrition knowledge may result in suboptimal practices, reducing strength, power, endurance, and immunity. Additionally, disordered attitudes can lead to dietary imbalances and an increased risk of injury. This study, conducted in Qazvin, Iran, examined athletes’ nutritional knowledge, attitudes, and practices. By addressing these factors, there is potential to enhance dietary behaviors and ultimately improve athletes’ performance.

Methods
The study employed a descriptive-analytical, cross-sectional design to investigate the nutritional knowledge, attitude, and practice (KAP) of professional athletes in Qazvin, Iran. A total of 320 purposefully selected professional athletes (68.13% male, 31.87% female) from various sports fields participated in the research. The data collection tool consisted of demographic questions and a KAP questionnaire, including 27 nutritional knowledge questions, 16 nutritional attitude questions, and 14 nutritional performance questions. The quota sampling method was used to estimate sample sizes. Data analysis was carried out by SPSS v.26 using one sample t-test, one-way ANOVA, and Pearson’s correlation coefficient test.

Results
The results showed that nutritional knowledge (the mean value was 79.594 ± 7.015 - the optimal knowledge level = 84) and attitude (the mean value was 23.347 ± 5.300 - the optimal attitude level = 26) for athletes are low, but their nutritional practice (the mean value was 21.788 ± 3.450 - the optimal performance level = 24) was moderate. Also, professional athletes’ nutritional knowledge, attitude, and practice were lower than normal (p < 0.05). Significant positive correlations were among knowledge, attitude, and practice (p < 0.05). However, there were no significant differences in nutritional knowledge, attitude, and practice among the subjects of different age groups, genders, and sports types (p > 0.05).

Conclusion
This study showed that the nutritional knowledge, attitude, and practice of professional Iranian athletes in Qazvin province were low; therefore, the implementation of more theoretical and applied nutrition education, such as using knowledge assessment tools and interventions, irrespective of their age, sport’s field, and gender, is compelling.
Functional independence, frailty and perceived quality of life in patients who developed delirium during ICU stay: a prospective cohort study
Authors: Lobo-Valbuena Beatriz , Molina Rosario , Castañeda-Vozmediano Raúl , Lopez de la Oliva Calvo Leire , Abella Ana , Garcia-Arias María-Mercedes , Salinas Gabiña Irene , Gordo Federico 
Published: December 2023

Abstract
Background
Survivors of critical illness are frequently left with a long-lasting disability. We hypothesised that patients who developed delirium during ICU stay, compared with patients who did not, would have worse health-related quality of life following a critical illness.

Methods
Prospective longitudinal observational and analytical study assessing functional independence, frailty and perceived quality of life measured with the Barthel Index, the Clinical Frailty Scale, and the SF-36, comparing patients who developed delirium during ICU stay and patients who did not. The questionnaires were used at different times during the follow-up (upon ICU admission, at ICU discharge, at hospital discharge and 2 years after hospital discharge).

Results
In a cohort of 1462 patients, we matched 93 patients who developed delirium (delirium group) with 93 patients who did not develop delirium (no-delirium group). Of 156 completed questionnaires (84.7%), we observed that (a) in each of the two groups of patients, the scores related to functional independence (Barthel Index) and frailty (Clinical Frailty Scale) tended to improve over time (p < 0.001), being consistently less favourable in the delirium group compared to the no-delirium group (p < 0.001); (b) the patients who developed delirium also presented lower scores on the SF-36 scale, these differences being statistically significant, and therefore evidencing a worse quality of life, with impact on both the psychological and social spheres (p < 0.001).

Conclusions
Patients who developed delirium had significantly lower scores 2 years after hospital discharge on the three used questionnaires, displaying a clear negative impact on the physical, psychological, and social dimensions. The study's results reinforce the need to support and strengthen the care of ICU survivors.
Research on the detection model of mental illness of online forum users based on convolutional network
Authors: Guo Yuliang , Zhang Zheng , Xu Xuejun 
Published: December 2023

AbstractRecently, there will be more than 4.62 billion social media users worldwide. A large number of users tend to publish personal emotional dynamics or express opinions on social media. These massive user data provide data support for the development of mental illness detection research and have achieved good results. However, it is difficult for current mental illness detection models to accurately identify key emotional features from a large number of posts issued by users to detect problem users. In view of the fact that the existing models cannot more accurately extract the words with high emotional contribution in the content of user posts, this paper proposes two hierarchical user post feature representation models, named Single-Gated LeakReLU-CNN (SGL-CNN) and Multi-Gated LeakyReLU-CNN (MGL-CNN). We leverage these 2 models to identify users with mental illness in online forums. For all posts published by each user within a certain time span, the model proposed in this paper can identify key emotional features in them and filter out other unimportant information as much as possible. In addition, the addition of gating units in this paper can significantly improve the performance of emotion detection tasks. The experimental results based on the task of RSDD dataset prove that the performance of the model proposed in this paper is superior to that of the existing methods.
Antibiotics and antibiotic-associated diarrhea: a real-world disproportionality study of the FDA adverse event reporting system from 2004 to 2022
Authors: Huang Haining , Li Lanfang , Wu Mingli , Liu Zhen , Zhao Yanyan , Peng Jing , Ren Xiaolei , Chen Shuai 
Published: December 2023

Abstract
Background
Our study aimed to assess the risk signals of antibiotic-associated diarrhea (AAD) caused by various antibiotics using real-world data and provide references for safe clinical applications.

Methods
We analyzed data extracted from the FDA Adverse Event Reporting System (FAERS) database, covering the period from the first quarter of 2004 to the third quarter of 2022. We computed the reporting odds ratio (ROR) for each antibiotic or antibiotic class to compare the signal difference. Furthermore, we also examined the differences in the onset times and outcomes of AAD caused by various antibiotics.

Results
A total of 5,397 reports met the inclusion requirements. Almost all antibiotics, except tobramycin and minocycline (ROR 0.98; 95%CI: 0.64–1.51 and 0.42; 95%CI: 0.16–1.11, respectively), showed a significant correlation with AAD. The analysis of the correlation between different classes of antibiotics and AAD revealed that lincomycins (ROR 29.19; 95%CI: 27.06–31.50), third-generation cephalosporins (ROR 15.96; 95%CI: 14.58–17.47), and first/second generation cephalosporins (ROR 15.29; 95%CI: 13.74–17.01) ranked the top three. The ROR values for antibiotics from the same class of antibiotics also varied greatly, with the ROR values for third-generation cephalosporins ranging from 9.97 to 58.59. There were also differences in ROR values between β-lactamase inhibitors and their corresponding β-lactamase drugs, such as amoxicillin-clavulanate (ROR = 13.31; 95%CI: 12.09–14.65) and amoxicillin (ROR = 6.50; 95%CI: 5.69–7.44). 91.35% of antibiotics have an onset time of less than four weeks.

Conclusions
There is a significant correlation between almost all antibiotics and AAD, particularly lincomycins and β-lactam antibiotics, as well as a different correlation within the same class. These findings offer valuable evidence for selecting antibiotics appropriately.
Glioblastoma pseudoprogression and true progression reveal spatially variable transcriptional differences
Authors: Wang Wesley , Tugaoen Jonah Domingo , Fadda Paolo , Toland Amanda Ewart , Ma Qin , Elder J. Brad , Giglio Pierre ,   James Cancer Center Integrated Neuro-Oncology Team, Giglio Pierre , Ong Shirley , Pillainayagam Clement , Gornanovich Justin , Gould Megan , Lima Judith , Lonser Russell , Elder Brad , Hardesty Douglas , Lucas Timothy , Ahmadian Saman , Kobalka Peter , Thomas Diana , Slone Wayne , Chakravarti Arnab , Raval Raju , Beyer Sasha , Palmer Joshua D. , Blakaj Dukagjin , Dawson Erica , Bell Erica , Otero José Javier 
Published: December 2023

AbstractPost-resection radiologic monitoring to identify areas of new or progressive enhancement concerning for cancer recurrence is critical during patients with glioblastoma follow-up. However, treatment-related pseudoprogression presents with similar imaging features but requires different clinical management. While pathologic diagnosis is the gold standard to differentiate true progression and pseudoprogression, the lack of objective clinical standards and admixed histologic presentation creates the needs to (1) validate the accuracy of current approaches and (2) characterize differences between these entities to objectively differentiate true disease. We demonstrated using an online RNAseq repository of recurrent glioblastoma samples that cancer-immune cell activity levels correlate with heterogenous clinical outcomes in patients. Furthermore, nCounter RNA expression analysis of 48 clinical samples taken from second neurosurgical resection supports that pseudoprogression gene expression pathways are dominated with immune activation, whereas progression is predominated with cell cycle activity. Automated image processing and spatial expression analysis however highlight a failure to apply these broad expressional differences in a subset of cases with clinically challenging admixed histology. Encouragingly, applying unsupervised clustering approaches over our segmented histologic images provides novel understanding of morphologically derived differences between progression and pseudoprogression. Spatially derived data further highlighted polarization of myeloid populations that may underscore the tumorgenicity of novel lesions. These findings not only help provide further clarity of potential targets for pathologists to better assist stratification of progression and pseudoprogression, but also highlight the evolution of tumor-immune microenvironment changes which promote tumor recurrence.
Cryo-EM structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer’s disease and cerebral amyloid angiopathy
Authors: Yang Yang , Murzin Alexey G. , Peak-Chew Sew , Franco Catarina , Garringer Holly J. , Newell Kathy L. , Ghetti Bernardino , Goedert Michel , Scheres Sjors H. W. 
Published: December 2023

AbstractWe used electron cryo-microscopy (cryo-EM) to determine the structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer’s disease and cerebral amyloid angiopathy. In agreement with previously reported structures, which were solved to a resolution of 4.4 Å, we found three types of filaments. However, our new structures, solved to a resolution of 2.4 Å, revealed differences in the sequence assignment that redefine the fold of Aβ40 peptides and their interactions. Filaments are made of pairs of protofilaments, the ordered core of which comprises D1–G38. The different filament types comprise one, two or three protofilament pairs. In each pair, residues H14–G37 of both protofilaments adopt an extended conformation and pack against each other in an anti-parallel fashion, held together by hydrophobic interactions and hydrogen bonds between main chains and side chains. Residues D1–H13 fold back on the adjacent parts of their own chains through both polar and non-polar interactions. There are also several additional densities of unknown identity. Sarkosyl extraction and aqueous extraction gave the same structures. By cryo-EM, parenchymal deposits of Aβ42 and blood vessel deposits of Aβ40 have distinct structures, supporting the view that Alzheimer’s disease and cerebral amyloid angiopathy are different Aβ proteinopathies.
Biomechanical effects of different staging and attachment designs in maxillary molar distalization with clear aligner: a finite element study
Authors: Gao Jie , Guo Donghui , Zhang Xu , Cheng Yuxun , Zhang Hao , Xu Yuerong , Jin Zuolin , Ma Yanning 
Published: December 2023

Abstract
Background
In the present study, the effects of distalizations of one and two molars with different step distances and attachment designs have been analyzed.

Methods
A 3D finite element analysis model has been developed in order to determine the tendency of tooth displacement and stress distribution with clear aligner treatment.

Results
Under the condition of single-molar distalization, when the step distance was set to 0.25 mm, the total displacement was 0.086 mm for central incisors, 0.080 mm for lateral incisors, 0.084 mm for canines, 0.102 mm for the first premolar and 0.076 mm for the second premolar. The von Mises stress of roots and the principal stress of the periodontal ligament was slightly lower than in the control group when the step distance was set to 0.130 mm. Under the condition of two-molar distalization, when the step distance was set to 0.130 mm, the total displacements for central incisors, lateral incisors and canines as well as both the first and second maxillary molars were basically the same as with a distance of 0.250 mm for one-molar distalization. In addition, when the step distance was 0.130 mm with two-molar distalization, the rotation center of the first and second molar was closer to the apex of the root indicating that the smaller step distance led to more bodily movement during the two-molar distalization. However, displacement tendencies of the first molar and the second molar were basically the same whether horizontal or vertical rectangular attachments were added.

Conclusions
A step distance of moving two molars to 0.130 mm can achieve the same reaction force on the anterior teeth as moving one molar 0.250 mm without effects on horizontal or vertical rectangular attachments.

Clinical relevance
Our results provide a theoretical basis and guidance for simultaneously moving two molars backward in clinical practice using a clear aligner.
16-channel SiPM high-frequency readout with time-over-threshold discrimination for ultrafast time-of-flight applications
Authors: Nadig Vanessa , Hornisch Matthias , Oehm Jakob , Herweg Katrin , Schulz Volkmar , Gundacker Stefan 
Published: December 2023

Abstract
Background
Over the past five years, ultrafast high-frequency (HF) readout concepts have advanced the timing performance of silicon photomultipliers (SiPMs). The shown impact in time-of-flight (TOF) techniques can further push the limits in light detection and ranging (LiDAR), time-of-flight positron-emission tomography (TOF-PET), time-of-flight computed tomography (TOF-CT) or high-energy physics (HEP). However, upscaling these electronics to a system-applicable, multi-channel readout, has remained a challenging task, posed by the use of discrete components and a high power consumption. To this day, there are no means to exploit the high TOF resolution of these electronics on system scale or to measure the actual timing performance limits of a full detector block.

Methods
In this work, we present a 16-channel HF readout board, including leading-edge discrimination and a linearized time-over-threshold (TOT) method, which is fully compatible with a high-precision time-to-digital converters (TDCs), such as the picoTDC developed at CERN. The discrete implementation allows ideal adaptation of this readout to a broad range of detection tasks. As a first step, the functionality of the circuit has been tested using the TOFPET2 ASIC as back-end electronics to emulate the TDC, also in view of its properties as a highly scalable data acquisition solution.

Results
The produced board is able to mitigate influences of baseline shifts in the TOFPET2 front end, which has been shown in experiments with a pulsed laser, increasing the achievable intrinsic coincidence timing resolution (CTR) of the TOFPET2 readout electronics from 70 ps (FWHM) to 62 ps (FWHM). Single-channel coincidence experiments including a $$\gamma$$
γ
-source, 2$$\times$$
×
2$$\times$$
×
3 mm$$^{3}$$

3

LYSO:Ce,Ca crystals and Broadcom NUV-MT SiPMs resulted in a CTR of 118 ps (FWHM). For a 4$$\times$$
×
4 matrix of 3.88$$\times$$
×
3.88$$\times$$
×
19 mm$$^{3}$$

3

LYSO:Ce,Ca crystals one-to-one coupled to a 4$$\times$$
×
4 array of Broadcom NUV-MT SiPMs, an average CTR of 223 ps (FWHM) was obtained.

Conclusion
The implemented 16-channel HF electronics are fully functionall and have a negligible influence on the timing performance of the back-end electronics used, here the TOFPET2 ASIC. The ongoing integration of the picoTDC with the 16-channel HF board is expected to further set the path toward sub-100 ps TOF-PET and sub-30ps TOF resolution for single-photon detection.
Induction of CYP3A activity by dexamethasone may not be strong, even at high doses: insights from a case of tacrolimus co-administration
Authors: Ohno Yoshiyuki , Oriyama Toyohito , Honda Akira , Kurokawa Mineo , Takada Tappei 
Published: December 2023

Abstract
Background
Dexamethasone (DEX) induces CYP3A activity in a concentration-dependent manner. However, no study has examined changes in the blood concentration of CYP3A substrate drugs when DEX is administered at high doses. Herein, we present a case in which tacrolimus (TAC), a typical CYP3A substrate drug, was co-administered with a chemotherapy regimen that included high-dose DEX.

Case presentation
A 71-year-old woman underwent liver transplantation for hepatocellular carcinoma 18 years prior to her inclusion in this case study. She was receiving TAC orally at 2 mg/day and had a stable trough blood concentration of approximately 4 ng/mL and a trough blood concentration/dose (C/D) ratio of approximately 2. The patient was diagnosed with post-transplant lymphoproliferative disease (histological type: Burkitt's lymphoma) after admission. Thereafter, the patient received cyclophosphamide-prednisolone (CP), followed by two courses of R-HyperCVAD (rituximab, cyclophosphamide, doxorubicin, vincristine, and DEX) and R-MA (rituximab, methotrexate, and cytarabine) replacement therapy. DEX (33 mg/day) was administered intravenously on days 1–4 and days 11–14 of R-HyperCVAD treatment, and aprepitant (APR) was administered on days 1–5 in both courses. The TAC C/D ratio decreased to approximately 1 on day 11 during both courses, and then increased. Furthermore, a decreasing trend in the TAC C/D ratio was observed after R-MA therapy. The decrease in the TAC C/D ratio was attributed to APR administration rather than to DEX.

Conclusion
The induction of CYP3A activity by a high dose of DEX may not be strong. The pharmacokinetic information on DEX and in vitro enzyme activity induction studies also suggested that CYP3A activity induction is not prominent under high-dose DEX treatment.