bluuebunny/crossref_metadata_2025_split huggingface dataset:
AECuration: Automated event curation for spike sorting
Authors: Li Xiang , Reddy Jay W , Jain Vishal , Forssell Mats , Ahmed Zabir , Chamanzar Maysamreza 
Published: January 2025

Abstract
Spike sorting is a commonly used analysis method for identifying single-units and multi-units from extracellular recordings. The extracellular recordings contain a mixture of signal components, such as neural and non-neural events, possibly due to motion and breathing artifacts or electrical interference. Identifying single and multi-unit spikes using a simple threshold-crossing method may lead to uncertainty in differentiating the actual neural spikes from non-neural spikes. The traditional method for classifying neural and non-neural units from spike sorting results is manual curation by a trained person. This subjective method suffers from human error and variability and is further complicated by the absence of ground truth in experimental extracellular recordings. Moreover, the manual curation process is time consuming and is becoming intractable due to the growing size and complexity of extracellular datasets. To address these challenges, we, for the first time, present a novel automatic curation method based on an autoencoder model, which is trained on features of simulated extracellular spike waveforms. The model is then applied to experimental electrophysiology datasets, where the reconstruction error is used as the metric for classifying neural and non-neural spikes. As an alternative to the traditional frequency domain and statistical techniques, our proposed method offers a time-domain evaluation model to automate the analysis of extracellular recordings based on learned time-domain features. The model exhibits excellent performance and throughput when applied to real-world extracellular datasets without any retraining, highlighting its generalizability. This method can be integrated into spike sorting pipelines as a pre-processing filtering step or a post-processing curation method.
Upgrade of the CMS Drift Tube electronics for the High Luminosity LHC
Authors: Redondo I. ,   the CMS collaboration
Published: January 2025

Abstract
The electronics of the CMS Drift Tubes (DT) chambers will be replaced to operate during High Luminosity (HL-LHC). In the upgraded architecture, optical links (lpGBT, VTRX+) send all signals to the backend, where complex logic running on FPGAs will process the data within trigger latency with precision enough to profit from the full chamber resolution, which in the present system is only possible offline. One of the sixty sectors of the detector was instrumented with the final version of the front-end boards (OBDTs, in two types) during the Winter stop 2022–23. After commissioning and integrating this setup in CMS operations during 2023, its stability has been tested in 2024 LHC collisions. Performance during 2024 campaign is summarized.
The services chain for the upgrade of the Inner Tracker Pixel detector of the ATLAS experiment. Full services from pixel modules to optical readout for the Outer Barrel sub-system
Authors: Zografos A. , Buytaert J. , Kuehn S. , Quadt A. , Skaf A. , Thys-dingou O. 
Published: January 2025

Abstract
For the high-luminosity upgrade of the ATLAS Inner Tracking detector, a new pixel detector will be installed to increase bandwidth and to cope with higher radiation, among other challenges. In this contribution, the design aspects and qualification of the data transmission from pixel modules to optical readout are presented. A focus is put on the data cable bundles and their performance for one of the Pixel sub-systems, the Outer Barrel. The development of a custom system for production testing of the bundles is discussed. Finally, in preparation of the detector integration, developments regarding functionality and connectivity testing are analyzed.
Resistive fine granularity Micromegas: characterization and performance for different spark protection resistive schemes
Authors: Alviggi M. , Biglietti M. , Camerlingo M.T. , Della Pietra M. , Di Donato C. , Di Nardo R. , Franchellucci S. , Iengo P. , Iodice M. , Petrucci F. , Sekhniaidze G. , Sessa M. 
Published: January 2025

Abstract
The aim of the presented work is the development of
single-stage amplification resistive Micro Pattern Gas Detectors
(MPGD) based on Micromegas technology with the following
characteristics: ability to efficiently operate up to 10 MHz/cm2
counting rate; scalability to large areas; fine granularity readout
with small pads of the order of mm2; good spatial and time
resolutions (below 100 um
and 10 ns, respectively). The miniaturization of the readout
elements and the optimization of the spark protection system, as
well as the stability and robustness under operation, are the
primary challenges of the project. Two families of resistive
patterns were realized using different techniques: pad-patterned
embedded resistors and double-layer of Diamond Like Carbon (DLC)
structures foils. The main difference between them is that for the
embedded resistors the charge is evacuated through independent pads,
for double-layer DLC the resistive layers are continuous and uniform
and the charge is evacuated through a network of dot-connections,
several millimetres apart. Using the DLC technique, a medium-size
detector with an active area of 400 cm2 was recently built and
tested, with the main results reported in this paper. Additionally,
a large module (40 cm2 x 50 cm2 active area), suitable
for tiling large systems in future experiments, has been
successfully realised and is currently undergoing testing and
performance studies.

The characterization and performance studies of the detectors were
conducted using radioactive sources and an X-rays generator, with
the detectors operated with various gas mixtures. A comparison of
the results obtained with different resistive layouts and
configurations is provided, with a particular focus on the response
under high-rate exposure. Key results on tracking and timing
performance from test-beam data for the latest constructed
medium-size detector are also presented.
Analysis of tail phenomena in micro-channel plate PMTs
Authors: Wu Qi , Ma Lishuang , Chen Lingyue , Lubsandorzhiev Bayarto K. , Qian Sen , Ushakov Nikita , Lubsandorzhiev Sultim 
Published: January 2025

Abstract
Photomultiplier Tubes (PMTs) employing micro-channel plate
(MCP) are a type of light-detection device designed for weak-light
conditions. The MCP multiplication structure has advantage over
traditional dynode structures due to its superior temporal
resolution and immunity to magnetic interference. The application of
atomic layer deposition (ALD) technology has significantly enhanced
the longevity of MCP-PMTs. Additionally, the collection efficiency
(CE) of MCP-PMTs is increased by coating the upper surface with high
secondary-electron emission materials. However, tails on charge and
transit time distribution are also observed which deteriorate the
charge and time resolution of the MCP-PMT. This can be explained by
the existance of the pre-multiplication events and elastically
recoiled events. In this paper, the waveforms for four types of
MCP-PMTs are analyzed, including the 20-inch MCP-PMT for JUNO, the
20-inch lotus-like MCP-PMT for LHAASO, the 2-inch 8×8-anodes
MCP-PMT and the 1-inch single-anode MCP-PMT. Under single-photon
detection environment, the full width at tenth maximum (FWTM) is
found to be an efficient parameter to realize the distinction of the
tails from the normal events for the 20-inch MCP-PMT. For the
small-sized FPMT, the origins for the tails in TT distribution is
also analyzed.
In-situ quality monitoring during embedded bioprinting using integrated microscopy and classical computer vision
Authors: Sergis Vasileios , Kelly Daniel , Pramanick Ankita , Britchfield Graham , Mason Karl , Daly Andrew C 
Published: January 2025

Abstract
Despite significant advances in bioprinting technology, current hardware platforms lack the capability for process monitoring and quality control. This limitation hampers the translation of the technology into industrial GMP-compliant manufacturing settings. As a key step towards a solution, we developed a novel bioprinting platform integrating a high-resolution camera for in-situ monitoring of extrusion outcomes during embedded bioprinting. Leveraging classical computer vision and image analysis techniques, we then created a custom software module for assessing print quality. This module enables quantitative comparison of printer outputs to input points of the computer-aided design model’s 2D projections, measuring area and positional accuracy. To showcase the platform’s capabilities, we then investigated compatibility with various bioinks, dyes, and support bath materials for both 2D and 3D print path trajectories. In addition, we performed a detailed study on how the rheological properties of granular support hydrogels impact print quality during embedded bioprinting, illustrating a practical application of the platform. Our results demonstrated that lower viscosity, faster thixotropy recovery, and smaller particle sizes significantly enhance print fidelity. This novel bioprinting platform, equipped with integrated process monitoring, holds great potential for establishing auditable and more reproducible biofabrication processes for industrial applications.
Corrigendum to “Influence of cyclic ignition and steady-state operation on a 1–2 A barium tungsten hollow cathode”
Authors: WANG 王 Fufeng 福锋 , MENG 孟 Tianhang 天航 , NING 宁 Zhongxi 中喜 , ZHU 朱 Ximing 悉铭 
Published: January 2025

Abstract
Figure 8(b) of the paper [Plasma Sci. Technol.
26 (2024) 125503] has been corrected. This modification does not affect the result presented in the paper.
The 14-3-3 protein CaTFT7 interacts with transcription factor CaHDZ27 to positively regulate pepper immunity against Ralstonia solanacearum
Authors: Mou Shaoliang , Chen Xiaodan , Cai Jiao , Zhang Tingting , Luo Tong , He Shuilin 
Published: January 2025

Abstract
Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting plants in the Solanaceae family. In our previous study, CaHDZ27 was shown to act crucially in the pepper defense response to R. solanacearum. However, the molecular basis underlying CaHDZ27 function remains unexplored. In this study, we demonstrate that CaHDZ27 is post-translationally regulated by the 14-3-3 protein CaTFT7, which functions as a positive regulator in pepper immunity against R. solanacearum. RT-qPCR analysis revealed that CaTFT7 is transcriptionally induced by R. solanacearum infection. The data from virus-induced gene silencing revealed that CaTFT7 positively affects pepper immunity, which was further confirmed by the data of CaTFT7-overexpressing Nicotiana benthamiana. CaTFT7 interacted with CaHDZ27, thereby promoting the stability of CaHDZ27 and enhancing CaHDZ27 binding to the promoter of cysteine-rich receptor-like protein kinase 5 (CaCRK5), a gene that positively affects pepper defense against R. solanacearum. The above data indicated that CaTFT7 enhanced CaHDZ27 stability and promoted its ability to activate pepper immunity, shedding light on the mechanisms underlying pepper resistance to bacterial wilt.
Symbiotic T6SS affects horizontal transmission of Paraburkholderia bonniea among Dictyostelium discoideum amoeba hosts
Authors: Chen Anna , Covitz Rachel M , Folsom Abigail A , Mu Xiangxi , Peck Ronald F , Noh Suegene 
Published: January 2025

Abstract
Three species of Paraburkholderia are able to form facultative symbiotic relationships with the amoeba, Dictyostelium discoideum. These symbiotic Paraburkholderia share a type VI secretion system (T6SS) that is absent in other close relatives. We tested the phenotypic and transcriptional effect of tssH ATPase gene disruption in P. bonniea on its symbiosis with D. discoideum. We hypothesized that the ∆tssH mutant would have a significantly reduced ability to affect host fitness or transmit itself from host to host. We found that the T6SS does not directly affect host fitness. Instead, wildtype P. bonniea had significantly higher rates of horizontal transmission compared to ∆tssH. In addition, we observed significant differences in the range of infection prevalence achieved by wildtype vs. ∆tssH symbionts over multiple host social stages in the absence of opportunities for environmental symbiont acquisition. Successful symbiont transmission significantly contributes to sustained symbiotic association. Therefore, the shared T6SS appears necessary for a long-term evolutionary relationship between D. discoideum and its Paraburkholderia symbionts. The lack of difference in host fitness outcomes was confirmed by indistinguishable host gene expression patterns between hosts infected by wildtype or ∆tssH P. bonniea in an RNA-seq time series. These data also provided insight into how Paraburkholderia symbionts may evade phagocytosis by its amoeba host. Most significantly, cellular oxidant detoxification and lysosomal hydrolase delivery appear to be subject to the push and pull of host-symbiont crosstalk.
Long-acting, progestin-based contraceptives and risk of breast, gynecological, and other cancers
Authors: Tuesley Karen M , Spilsbury Katrina , Pearson Sallie-Anne , Donovan Peter , Obermair Andreas , Coory Michael D , Ali Sitwat , Pandeya Nirmala , Stewart Louise , Jordan Susan J , Webb Penelope M 
Published: January 2025

Abstract

Background
Use of long-acting, reversible contraceptives has increased over the past 20 years, but an understanding of how they could influence cancer risk is limited.

Methods
We conducted a nested case-control study among a national cohort of Australian women (n = 176 601 diagnosed with cancer between 2004 and 2013; 882 999 matched control individuals) to investigate the associations between the levonorgestrel intrauterine system, etonogestrel implants, depot-medroxyprogesterone acetate and cancer risk and compared these results with the oral contraceptive pill. We used conditional logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI).

Results
Levonorgestrel intrauterine system and etonogestrel implant use was associated with breast cancer risk (OR = 1.26, 95% CI = 1.21 to 1.31, and OR = 1.24, 95% CI = 1.17 to 1.32, respectively), but depot-medroxyprogesterone acetate was not, except when used for 5 or more years (OR = 1.23, 95% CI = 0.95 to 1.59). Reduced risks were seen for levonorgestrel intrauterine system (≥1 years of use) in endometrial cancer (OR = 0.80, 95% CI = 0.65 to 0.99), ovarian cancer (OR = 0.71, 95% CI = 0.57 to 0.88), and cervical cancer (OR = 0.62, 95% CI = 0.51 to 0.75); for etonogestrel implant in endometrial cancer (OR = 0.21, 95% CI = 0.13 to 0.34) and ovarian cancer (OR = 0.76, 95% CI = 0.57 to 1.02); and for depot-medroxyprogesterone acetate in endometrial cancer (OR = 0.21, 95% CI = 0.13 to 0.34). Although levonorgestrel intrauterine system, etonogestrel implant and depot-medroxyprogesterone acetate were all associated with increased cancer risk overall, for etonogestrel implant, the risk returned to baseline after cessation, similar to the oral contraceptive pill. We were unable to adjust for all potential confounders, but sensitivity analyses suggested that adjusting for parity, smoking, and obesity would not have materially changed our findings.

Conclusion
Long-acting, reversible contraceptives have similar cancer associations to the oral contraceptive pill (reduced endometrial and ovarian cancer risks and short-term increased breast cancer risk). This information may be helpful to women and their physicians when discussing contraception options.
Benchmarking the Efficacy of Salvage Systemic Therapies for Recurrent Meningioma: A RANO Group Systematic Review and Meta-analysis to Guide Clinical Trial Design
Authors: Kotecha Rupesh , Akdemir Eyub Y , Kutuk Tugce , Ilgin Can , Ahluwalia Manmeet S , Bi Wenya L , Blakeley Jaishri , Dixit Karan S , Dunn Ian F , Galanis Evanthia , Galldiks Norbert , Huang Raymond Y , Johnson Derek R , Kaley Thomas J , Kamson David O , Kurz Sylvia C , McDermott Michael W , Odia Yazmin , Preusser Matthias , Raizer Jeffrey , Reardon David A , Rogers C Leland , Ruda Roberta , Schiff David , Vogelbaum Michael A , Weller Michael , Wen Patrick Y , Mehta Minesh P 
Published: January 2025

Abstract

Background
Despite advances in our understanding of the molecular underpinnings of meningioma progression and innovations in systemic and local treatments, recurrent meningiomas remain a substantial therapeutic challenge. The objective of this systematic review and meta-analysis is to provide a historical baseline, contemporary analysis, and propose a “rate of probable interest” to inform future clinical trial design and development on behalf of the RANO meningioma group.

Methods
PubMed, ClinicalTrials.gov, and ASCOpubs databases were screened for clinical trials evaluating the activity of systemic therapies for adults with recurrent meningiomas. The pooled progression-free survival at 6-months and 1-year (PFS-6 and PFS-1 year) values were calculated using the random effects technique with I-squared indices.

Results
The pooled PFS-6 and PFS-1 year rates for recurrent WHO grade 1 meningiomas were 43.6% (95% CI: 22.7-67.0%, I2=80%) and 21.7% (95% CI: 6.2-53.9%, I2=76%), and for grade 2-3 meningiomas, the PFS-6 was 38.0% (95% CI: 28.3-48.8%, I2=68%). In targeted therapy group, PFS-6 and PFS-1 year rates stood at 62.0% (I2=58%) and 49.0% (I2=63%) for grade 1, while for grade 2-3 tumors, the PFS-6 rate with targeted therapy and immunotherapy was 42.1% (I²=60%) and 46.0% (I²=0%), respectively. The benchmarks were set at 67% and 54% for PFS-6 and PFS-1 year for grade 1 tumors, and PFS-6 of 49% for grade 2-3 tumors.

Conclusions
Several studies have reported outcomes in patients with recurrent meningiomas testing a variety of agents with modest, but variable and progressively increasing activity. In this context, we recommend new benchmarks for future trials to define efficacy of future investigational therapies.
Effect of Patient Age on Decisional Regret After Laparoscopic Hysterectomy
Authors: King Nathan R. , Zeccola Alison M. , Wang Li , Harris John A. , Foley Christine E. 
Published: January 2025

OBJECTIVE:
To compare long-term decision regret between younger (30 years or younger) and older (31–49 years) patients who underwent laparoscopic hysterectomy for benign disease.

METHODS:
We conducted a matched retrospective cohort study to analyze patients who underwent laparoscopic hysterectomies for benign indications from 2009 to 2016. Respondents completed surveys including two validated decision regret scales: one measuring surgical decision regret and the other measuring loss-of-fertility regret. Participant aged was dichotomized as 30 years or younger and 31–49 years. Chi square, Fisher exact, and Wilcoxon rank sum tests and logistic regression were used to compare groups.

RESULTS:
Two hundred eighty-seven participants were successfully contacted, and 241 completed the survey (84.0%). Seventy-seven respondents (32.0%) were aged 30 years or younger, and 164 (68.0%) were aged 31–49 years. The average time since surgery was 7.2 years (±2.2 years; range 3.7–12.1 years). Participants aged 30 years or younger regretted both undergoing surgery (32.5% vs 9.1%, P<.001; OR 4.8, 95% CI, 2.3–9.8) and loss of fertility (39.0% vs 13.4%, P<.001, OR 4.1, 95% CI, 2.2–7.8) at significantly higher rates than participants aged 31–49 years. Overall, 83.1% of younger participants agreed that hysterectomy was the right choice compared with 97% of older participants (P<.001). Higher rates of surgical and loss-of-fertility regret were seen in participants with self-reported pelvic pain (P=.003, P=.011), preoperative diagnosis of endometriosis (P=.037, P=.046), and postoperative complications (P=.043, P<.001). Although time since hysterectomy did not affect rate of surgical regret (P=.138), participants further from their hysterectomies had lower rates of loss-of-fertility regret (P=.003). Patient age remained significantly associated with both surgical regret (adjusted OR 2.9 (95% CI, 1.3–6.5) and loss-of-fertility regret (adjusted OR 2.8 (95% CI, 1.3–6.0) on multivariable logistic regression.

CONCLUSION:
Participants aged 30 years or younger were more likely to regret their decision to undergo hysterectomy than participants aged 31–49 years, regardless of parity, prior sterilization, or previous treatment.
Using machine learning models to identify severe subjective cognitive decline and related factors in nurses during the menopause transition: a pilot study
Authors: Zhao Xiangyu , Shen Xiaona , Jia Fengcai , He Xudong , Zhao Di , Li Ping 
Published: January 2025

Abstract

Objective
This study aims to develop and validate a machine learning model for identifying individuals within the nursing population experiencing severe subjective cognitive decline (SCD) during the menopause transition, along with their associated factors.

Methods
A secondary analysis was performed using cross-sectional data from 1,264 nurses undergoing the menopause transition. The data set was randomly split into training (75%) and validation sets (25%), with the Bortua algorithm employed for feature selection. Seven machine learning models were constructed and optimized. Model performance was assessed using area under the receiver operating characteristic curve, accuracy, sensitivity, specificity, and F1 score. Shapley Additive Explanations analysis was used to elucidate the weights and characteristics of various factors associated with severe SCD.

Results
The average SCD score among nurses in the menopause transition was (5.38 ± 2.43). The Bortua algorithm identified 13 significant feature factors. Among the seven models, the support vector machine exhibited the best overall performance, achieving an area under the receiver operating characteristic curve of 0.846, accuracy of 0.789, sensitivity of 0.753, specificity of 0.802, and an F1 score of 0.658. The two variables most strongly associated with SCD were menopausal symptoms and the stage of menopause.

Conclusions
The machine learning models effectively identify individuals with severe SCD and the related factors associated with severe SCD in nurses during the menopause transition. These findings offer valuable insights for the management of cognitive health in women undergoing the menopause transition.