bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parsing altered gray matter morphology of depression using a framework integrating the normative model and non-negative matrix factorization
Authors: Han Shaoqiang , Cui Qian , Zheng Ruiping , Li Shuying , Zhou Bingqian , Fang Keke , Sheng Wei , Wen Baohong , Liu Liang , Wei Yarui , Chen Huafu , Chen Yuan , Cheng Jingliang , Zhang Yong 
Published: July 2023

AbstractThe high inter-individual heterogeneity in individuals with depression limits neuroimaging studies with case-control approaches to identify promising biomarkers for individualized clinical decision-making. We put forward a framework integrating the normative model and non-negative matrix factorization (NMF) to quantitatively assess altered gray matter morphology in depression from a dimensional perspective. The proposed framework parses altered gray matter morphology into overlapping latent disease factors, and assigns patients distinct factor compositions, thus preserving inter-individual variability. We identified four robust disease factors with distinct clinical symptoms and cognitive processes in depression. In addition, we showed the quantitative relationship between the group-level gray matter morphological differences and disease factors. Furthermore, this framework significantly predicted factor compositions of patients in an independent dataset. The framework provides an approach to resolve neuroanatomical heterogeneity in depression.
Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling
Authors: Li Shang , Zhai Junyu , Chu Weiwei , Geng Xueying , Wang Dongshuang , Jiao Luwei , Lu Gang , Chan Wai-Yee , Sun Kang , Sun Yun , Chen Zi-Jiang , Du Yanzhi 
Published: July 2023

AbstractKnowledge gaps that limit the development of therapies for polycystic ovary syndrome (PCOS) concern various environmental factors that impact clinical characteristics. Circadian dysrhythmia contributes to glycometabolic and reproductive hallmarks of PCOS. Here, we illustrated the amelioration ofLimosilactobacillus reuteri(L. reuteri) on biorhythm disorder-ignited dyslipidemia of PCOS via a microbiota-metabolite-liver axis. A rat model of long-term (8 weeks) darkness treatment was used to mimic circadian dysrhythmia-induced PCOS. Hepatic transcriptomics certified by in vitro experiments demonstrated that increased hepatic galanin receptor 1 (GALR1) due to darkness exposure functioned as a critical upstream factor in the phosphoinositide 3-kinase (PI3K)/protein kinase B pathway to suppress nuclear receptors subfamily 1, group D, member 1 (NR1D1) and promoted sterol regulatory element binding protein 1 (SREBP1), inducing lipid accumulation in the liver. Further investigations figured out a restructured microbiome-metabolome network followingL. reuteriadministration to protect darkness rats against dyslipidemia. Notably,L. reuteriintervention resulted in the decrease ofClostridium sensu stricto 1andRuminococcaceae UCG-010as well as gut microbiota-derived metabolite capric acid, which could further inhibit GALR1-NR1D1-SREBP1 pathway in the liver. In addition, GALR antagonist M40 reproduced similar ameliorative effects asL. reuterito protect against dyslipidemia. While exogenous treatment of capric acid restrained the protective effects ofL. reuteriin circadian disruption-induced PCOS through inhibiting GALR1-dependent hepatic lipid metabolism. These findings purport thatL. reutericould serve for circadian disruption-associated dyslipidemia. Manipulation ofL. reuteri–capric acid–GALR1 axis paves way for clinical therapeutic strategies to prevent biorhythm disorder-ignited dyslipidemia in PCOS women.
Proteome wide association studies of LRRK2 variants identify novel causal and druggable proteins for Parkinson’s disease
Authors: Phillips Bridget , Western Daniel , Wang Lihua , Timsina Jigyasha , Sun Yichen , Gorijala Priyanka , Yang Chengran , Do Anh , Nykänen Niko-Petteri , Alvarez Ignacio , Aguilar Miquel , Pastor Pau , Morris John C. , Schindler Suzanne E. , Fagan Anne M. , Puerta Raquel , García-González Pablo , de Rojas Itziar , Marquié Marta , Boada Mercè , Ruiz Agustin , Perlmutter Joel S. ,   Dominantly Inherited Alzheimer Network (DIAN) Consortia, Ibanez Laura , Perrin Richard J. , Sung Yun Ju , Cruchaga Carlos 
Published: July 2023

AbstractCommon and rare variants in the LRRK2 locus are associated with Parkinson’s disease (PD) risk, but the downstream effects of these variants on protein levels remain unknown. We performed comprehensive proteogenomic analyses using the largest aptamer-based CSF proteomics study to date (7006 aptamers (6138 unique proteins) in 3107 individuals). The dataset comprised six different and independent cohorts (five using the SomaScan7K (ADNI, DIAN, MAP, Barcelona-1 (Pau), and Fundació ACE (Ruiz)) and the PPMI cohort using the SomaScan5K panel). We identified eleven independent SNPs in the LRRK2 locus associated with the levels of 25 proteins as well as PD risk. Of these, only eleven proteins have been previously associated with PD risk (e.g., GRN or GPNMB). Proteome-wide association study (PWAS) analyses suggested that the levels of ten of those proteins were genetically correlated with PD risk, and seven were validated in the PPMI cohort. Mendelian randomization analyses identified GPNMB, LCT, and CD68 causal for PD and nominate one more (ITGB2). These 25 proteins were enriched for microglia-specific proteins and trafficking pathways (both lysosome and intracellular). This study not only demonstrates that protein phenome-wide association studies (PheWAS) and trans-protein quantitative trail loci (pQTL) analyses are powerful for identifying novel protein interactions in an unbiased manner, but also that LRRK2 is linked with the regulation of PD-associated proteins that are enriched in microglial cells and specific lysosomal pathways.
Controllable tunability of a Chern number within the electronic-nuclear spin system in diamond
Authors: Lee Junghyun , Arai Keigo , Zhang Huiliang , Ku Mark J. H. , Walsworth Ronald L. 
Published: July 2023

AbstractChern numbers characterize topological phases in a wide array of physical systems. However, the resilience of system topology to external perturbations makes it challenging experimentally to investigate transitions between different phases. In this study, we demonstrate the transitions of a Chern number from 0 to 3, synthesized in an electronic-nuclear spin system associated with the nitrogen-vacancy (NV) centre in diamond. The Chern number is characterized by the number of degeneracies enclosed in a control Hamiltonian parameter sphere. Topological transitions between different phases are realized by varying the radius and offset of the sphere such that the Chern number changes. We show that the measured topological phase diagram is consistent with numerical calculations and can also be mapped onto an interacting three-qubit system. The NV system may also allow access to even higher Chern numbers, which could be applied to exploring exotic topology or topological quantum information.
Strong majorization uncertainty relations and experimental verifications
Authors: Yuan Yuan , Xiao Yunlong , Hou Zhibo , Fei Shao-Ming , Gour Gilad , Xiang Guo-Yong , Li Chuan-Feng , Guo Guang-Can 
Published: July 2023

AbstractIn spite of enormous theoretical and experimental progress in quantum uncertainty relations, the experimental investigation of the most current, and universal formalism of uncertainty relations, namely majorization uncertainty relations (MURs), has not been implemented yet. A major problem is that previous studies of majorization uncertainty relations mainly focus on their mathematical expressions, leaving the physical interpretation of these different forms unexplored. To address this problem, we employ a guessing game formalism to reveal physical differences between diverse forms of majorization uncertainty relations. Furthermore, we tighter the bounds of MURs by using flatness processes. Finally, we experimentally verify strong MURs in the photonic system to benchmark our theoretical results.
Optical and structural characterization of femtosecond laser written micro-structures in germanate glass
Authors: Zaiter Rayan , Lancry Matthieu , Fargues Alexandre , Adamietz Frédéric , Dussauze Marc , Rodriguez Vincent , Poumellec Bertrand , Cardinal Thierry 
Published: July 2023

AbstractWe report on direct femtosecond laser writing in zinc barium gallo-germanate glasses. A combination of spectroscopic techniques allows to progress in the understanding of the mechanisms taking place depending on the energy. In the first regime (type I, isotropic local index change) up to 0.5 µJ, the main occurrence is the generation of charge traps inspected by luminescence, together with separation of charges detected by polarized second harmonic generation measurements. At higher pulse energies notably at the threshold corresponding to 0.8 µJ or in the second regime (type II modifications corresponding to nanograting formation energy domain), the main occurrence is a chemical change and re-organization of the network evidenced by the appearance of molecular O2 seen in the Raman spectra. In addition, the polarization dependence of the second harmonic generation in type II indicates that the organization of nanogratings may be perturbed by the laser-imprinted electric field.
Decentralized environmental applications of a smartphone-based method for chemical oxygen demand and color analysis
Authors: Cardozo Jussara Câmara , Barbosa Segundo Inalmar D. , Galvão Edney R. V. P. , da Silva Djalma R. , dos Santos Elisama V. , Martínez-Huitle Carlos A. 
Published: July 2023

AbstractThis study is focused on a proposal of a smartphone imaging-based quantification for providing a simple and rapid method for the analysis of chemical oxygen demand (COD) and color throughout the use of the HSV and/or RGB model in digital devices. For COD, calibration curves were done based on the theoretical values of potassium biphthalate for a proper comparison between the spectrophotometer and the smartphone techniques. The smartphone camera and application attain an average accuracy higher than the analysis in the spectrophotometer (98.3 and 96.2%, respectively). In the color analysis, it was demonstrated that only the UV–vis bands measurement is not feasible to perform the real abatement of the dye in the water because the limiting concentration that allows obtaining a linear relationship in this equipment related to the dye concentration is about 10 mg L−1. Above this value, the spectrophotometer can not reach the real difference of color in the solution. Meanwhile, the smartphone method by using the camera reaches linearity until 50 mg L−1. From an environmental point of view, smartphones have been used for monitoring several organic and inorganic pollutants, however, no attempts have been published related to their use to evaluate the color and COD during wastewater treatment. Therefore, this investigation also aims to assess the utilization of these methods, for the first time, when high-colored water polluted by methylene blue (MB) was electrochemically treated by using a boron-dopped diamond (BDD) as the anode, with different current densities (j = 30, 45, 60, and 90 mA cm−2). COD and color abatement results clearly showed that different organic matter/color removal efficiencies were achieved, depending on the j used. All the results are aligned with the studies already available in the literature, with the total removal of color in 120 min of electrolysis with 60 and 90 mA cm−2, and almost 80% of COD abatement with the higher j. Moreover, samples of real effluent from beauty salons were compared, with standard deviation varying from only 3 to 40 mg O2 L−1, which is acceptable for COD values close to 2000. Finally, the methods here presented can be a great benefit for public water monitoring policies, since it is cheap and has a decentralized characteristic, given that smartphones are very common and portable devices.
Pharmacokinetics, biodistribution and toxicology of novel cell-penetrating peptides
Authors: Reveret L. , Leclerc M. , Morin F. , Émond V. , Calon F. 
Published: July 2023

AbstractCell-penetrating peptides (CPPs) have been used in basic and preclinical research in the past 30 years to facilitate drug delivery into target cells. However, translation toward the clinic has not been successful so far. Here, we studied the pharmacokinetic (PK) and biodistribution profiles of Shuttle cell-penetrating peptides (S-CPP) in rodents, combined or not with an immunoglobulin G (IgG) cargo. We compared two enantiomers of S-CPP that contain both a protein transduction domain and an endosomal escape domain, with previously shown capacity for cytoplasmic delivery. The plasma concentration versus time curve of both radiolabelled S-CPPs required a two-compartment PK analytical model, which showed a fast distribution phase (t1/2α ranging from 1.25 to 3 min) followed by a slower elimination phase (t1/2β ranging from 5 to 15 h) after intravenous injection. Cargo IgG combined to S-CPPs displayed longer elimination half-life, of up to 25 h. The fast decrease in plasma concentration of S-CPPs was associated with an accumulation in target organs assessed at 1 and 5 h post-injection, particularly in the liver. In addition, in situ cerebral perfusion (ISCP) of L-S-CPP yielded a brain uptake coefficient of 7.2 ± 1.1 µl g−1 s−1, consistent with penetration across the blood–brain barrier (BBB), without damaging its integrity in vivo. No sign of peripheral toxicity was detected either by examining hematologic and biochemical blood parameters, or by measuring cytokine levels in plasma. In conclusion, S-CPPs are promising non-toxic transport vectors for improved tissue distribution of drug cargos in vivo.
Automated machine learning (AutoML) can predict 90-day mortality after gastrectomy for cancer
Authors: SenthilKumar Gopika , Madhusudhana Sharadhi , Flitcroft Madelyn , Sheriff Salma , Thalji Samih , Merrill Jennifer , Clarke Callisia N. , Maduekwe Ugwuji N. , Tsai Susan , Christians Kathleen K. , Gamblin T. Clark , Kothari Anai N. 
Published: July 2023

AbstractEarly postoperative mortality risk prediction is crucial for clinical management of gastric cancer. This study aims to predict 90-day mortality in gastric cancer patients undergoing gastrectomy using automated machine learning (AutoML), optimize models for preoperative prediction, and identify factors influential in prediction. National Cancer Database was used to identify stage I–III gastric cancer patients undergoing gastrectomy between 2004 and 2016. 26 features were used to train predictive models using H2O.ai AutoML. Performance on validation cohort was measured. In 39,108 patients, 90-day mortality rate was 8.8%. The highest performing model was an ensemble (AUC = 0.77); older age, nodal ratio, and length of inpatient stay (LOS) following surgery were most influential for prediction. Removing the latter two parameters decreased model performance (AUC 0.71). For optimizing models for preoperative use, models were developed to first predict node ratio or LOS, and these predicted values were inputted for 90-day mortality prediction (AUC of 0.73–0.74). AutoML performed well in predicting 90-day mortality in a larger cohort of gastric cancer patients that underwent gastrectomy. These models can be implemented preoperatively to inform prognostication and patient selection for surgery. Our study supports broader evaluation and application of AutoML to guide surgical oncologic care.
Jelly-Z: swimming performance and analysis of twisted and coiled polymer (TCP) actuated jellyfish soft robot
Authors: Matharu Pawandeep Singh , Gong Pengyao , Guntaka Koti Pramod Reddy , Almubarak Yara , Jin Yaqing , Tadesse Yonas T. 
Published: July 2023

AbstractMonitoring, sensing, and exploration of over 70% of the Earth’s surface that is covered with water is permitted through the deployment of underwater bioinspired robots without affecting the natural habitat. To create a soft robot actuated with soft polymeric actuators, this paper describes the development of a lightweight jellyfish-inspired swimming robot, which achieves a maximum vertical swimming speed of 7.3 mm/s (0.05 body length/s) and is characterized by a simple design. The robot, named Jelly-Z, utilizes a contraction–expansion mechanism for swimming similar to the motion of a Moon jellyfish. The objective of this paper is to understand the behavior of soft silicone structure actuated by novel self-coiled polymer muscles in an underwater environment by varying stimuli and investigate the associated vortex for swimming like a jellyfish. To better understand the characteristics of this motion, simplified Fluid–structure simulation, and particle image velocimetry (PIV) tests were conducted to study the wake structure from the robot’s bell margin. The thrust generated by the robot was also characterized with a force sensor to ascertain the force and cost of transport (COT) at different input currents. Jelly-Z is the first robot that utilized twisted and coiled polymer fishing line (TCPFL) actuators for articulation of the bell and showed successful swimming operations. Here, a thorough investigation on swimming characteristics in an underwater setting is presented theoretically and experimentally. We found swimming metrics of the robot are comparable with other jellyfish-inspired robots that have utilized different actuation mechanisms, but the actuators used here are scalable and can be made in-house relatively easily, hence paving way for further advancements into the use of these actuators.
Overactive bladder syndrome symptoms in youth with abdominal pain-associated disorders of gut–brain interaction
Authors: Friesen Hunter J. , Thompson Pierce , Schurman Jennifer V. , Colombo Jennifer M. , Friesen Craig A. 
Published: July 2023

AbstractThe purpose of the current study was to assess the frequency of overactive bladder syndrome (OBS) symptoms and their relationship to gastrointestinal symptoms in youth with abdominal pain-associated disorders of gut–brain interaction (AP-DGBI). This is a retrospective study of 226 youth diagnosed with an AP-DGBI. As part of standard care, all patients completed a symptom questionnaire regarding gastrointestinal and non-gastrointestinal symptoms including increased urinary frequency, nighttime urination, and urinary urgency. Overall, 54% of patients reported at least one OBS symptom. Increased frequency of urination was reported by 19%, urinary urgency by 34%, and nighttime urination by 36%. Increased frequency of urination and urinary urgency were associated with a change in stool form, a change in stool frequency, and in those fulfilling criteria for IBS. Increased frequency of urination was reported more frequently in those reporting predominantly loose stools (33% vs. 12%). Urinary symptoms are common in youth with AP-DGBI. Increased urinary frequency and urinary urgency are specifically associated with IBS, with increased urinary frequency being primarily associated with diarrhea predominant IBS. Further studies are needed to determine the impact of OBS on AP-DGBI severity and quality of life, and whether they impact DGBI treatment.
Estimating vaccine coverage in conflict settings using geospatial methods: a case study in Borno state, Nigeria
Authors: Sbarra Alyssa N. , Rolfe Sam , Haeuser Emily , Nguyen Jason Q. , Adamu Aishatu , Adeyinka Daniel , Ajumobi Olufemi , Akunna Chisom , Amusa Ganiyu , Dahiru Tukur , Ekholuenetale Michael , Esezobor Christopher , Fowobaje Kayode , Hay Simon I. , Ibeneme Charles , Ibitoye Segun Emmanuel , Ilesanmi Olayinka , Kayode Gbenga , Krohn Kris , Lim Stephen S. , Medeiros Lyla E. , Mohammed Shafiu , Nwatah Vincent , Okoro Anselm , Olagunju Andrew T. , Olusanya Bolajoko O. , Osarenotor Osayomwanbo , Owolabi Mayowa , Pickering Brandon , Sufiyan Mu’awiyyah Babale , Uzochukwu Benjamin , Walker Ally , Mosser Jonathan F. 
Published: July 2023

AbstractReliable estimates of subnational vaccination coverage are critical to track progress towards global immunisation targets and ensure equitable health outcomes for all children. However, conflict can limit the reliability of coverage estimates from traditional household-based surveys due to an inability to sample in unsafe and insecure areas and increased uncertainty in underlying population estimates. In these situations, model-based geostatistical (MBG) approaches offer alternative coverage estimates for administrative units affected by conflict. We estimated first- and third-dose diphtheria-tetanus-pertussis vaccine coverage in Borno state, Nigeria, using a spatiotemporal MBG modelling approach, then compared these to estimates from recent conflict-affected, household-based surveys. We compared sampling cluster locations from recent household-based surveys to geolocated data on conflict locations and modelled spatial coverage estimates, while also investigating the importance of reliable population estimates when assessing coverage in conflict settings. These results demonstrate that geospatially-modelled coverage estimates can be a valuable additional tool to understand coverage in locations where conflict prevents representative sampling.
X-ray driven and intrinsic dynamics in protein gels
Authors: Timmermann Sonja , Anthuparambil Nimmi Das , Girelli Anita , Begam Nafisa , Kowalski Marvin , Retzbach Sebastian , Senft Maximilian Darius , Akhundzadeh Mohammad Sayed , Poggemann Hanna-Friederike , Moron Marc , Hiremath Anusha , Gutmüller Dennis , Dargasz Michelle , Öztürk Özgül , Paulus Michael , Westermeier Fabian , Sprung Michael , Ragulskaya Anastasia , Zhang Fajun , Schreiber Frank , Gutt Christian 
Published: July 2023

AbstractWe use X-ray photon correlation spectroscopy to investigate how structure and dynamics of egg white protein gels are affected by X-ray dose and dose rate. We find that both, changes in structure and beam-induced dynamics, depend on the viscoelastic properties of the gels with soft gels prepared at low temperatures being more sensitive to beam-induced effects. Soft gels can be fluidized by X-ray doses of a few kGy with a crossover from stress relaxation dynamics (Kohlrausch–Williams–Watts exponents $$k \approx 1.5$$

k
≈
1.5

to 2) to typical dynamical heterogeneous behavior ($$k<$$

k
<

1) while the high temperature egg white gels are radiation-stable up to doses of 15 kGy with $$k\ge 1.5$$

k
≥
1.5

. For all gel samples we observe a crossover from equilibrium dynamics to beam induced motion upon increasing X-ray fluence and determine the resulting fluence threshold values $$\Phi _D$$

Φ
D

. Surprisingly small threshold values of $$\Phi _D=(3 \pm 2)\times 10^{-3} \,\textrm{ph}\,$$

Φ
D

=

(
3
±
2
)

×

10

-
3

ph

s$$^{-1}$$

-
1

nm$$^{-2}$$

-
2

can drive the dynamics in the soft gels while for stronger gels this threshold is increased to $$\Phi _D=(0.9 \pm 0.3) \,\textrm{ph}$$

Φ
D

=

(
0.9
±
0.3
)

ph

s$$^{-1}$$

-
1

nm$$^{-2}$$

-
2

. We explain our observations with the viscoelastic properties of the materials and can connect the threshold dose for structural beam damage with the dynamic properties of beam-induced motion. Our results suggest that soft viscoelastic materials can display pronounced X-ray driven motion even for low X-ray fluences. This induced motion is not detectable by static scattering as it appears at dose values well below the static damage threshold. We show that intrinsic sample dynamics can be separated from X-ray driven motion by measuring the fluence dependence of the dynamical properties.