bluuebunny/crossref_metadata_2025_split huggingface dataset:
LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing
Authors: Duan Junbo , Zhao Xinrui , Wu Xiaoming 
Published: June 2024

Abstract
Single-cell sequencing has revolutionized our ability to dissect the heterogeneity within tumor populations. In this study, we present LoRA-TV (Low Rank Approximation with Total Variation), a novel method for clustering tumor cells based on the read depth profiles derived from single-cell sequencing data. Traditional analysis pipelines process read depth profiles of each cell individually. By aggregating shared genomic signatures distributed among individual cells using low-rank optimization and robust smoothing, the proposed method enhances clustering performance. Results from analyses of both simulated and real data demonstrate its effectiveness compared with state-of-the-art alternatives, as supported by improvements in the adjusted Rand index and computational efficiency.
Flexible parsing, interpretation, and editing of technical sequences with splitcode
Authors: Sullivan Delaney K , Pachter Lior 
Published: June 2024

Abstract

Motivation
Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed.

Results
We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.

Availability and implementation
The splitcode program is available at http://github.com/pachterlab/splitcode.
On some algorithms for estimation in Gaussian graphical models
Authors: Højsgaard S , Lauritzen S 
Published: June 2024

Abstract
In Gaussian graphical models, the likelihood equations must typically be solved iteratively. This paper investigates two algorithms: a version of iterative proportional scaling, which avoids inversion of large matrices, and an algorithm based on convex duality and operating on the covariance matrix by neighbourhood coordinate descent, which corresponds to the graphical lasso with zero penalty. For large, sparse graphs, the iterative proportional scaling algorithm appears feasible and has simple convergence properties. The algorithm based on neighbourhood coordinate descent is extremely fast and less dependent on sparsity, but needs a positive-definite starting value to converge. We provide an algorithm for finding such a starting value for graphs with low colouring number. As a consequence, we also obtain a simplified proof of existence of the maximum likelihood estimator in such cases.
Understanding decision-making for and against oncoplastic breast-conserving surgery as an alternative to a mastectomy in early breast cancer: UK ANTHEM qualitative study
Authors: Davies Charlotte , Conefrey Carmel , Mills Nicola , Fairbrother Patricia , Holcombe Chris , Whisker Lisa , Skillman Joanna , White Paul , MacMillan Douglas , Comins Charles , Hollingworth William , Potter Shelley 
Published: June 2024

Abstract

Background
Oncoplastic breast-conserving surgery may allow women with early breast cancer to avoid a mastectomy, but many women undergo more extensive surgery, even when breast-conserving options are offered. The aim of the ANTHEM qualitative study was to explore factors influencing women’s surgical decision-making for and against oncoplastic breast-conserving surgery.

Methods
Semi-structured interviews were conducted with a purposive sample of women who had received either oncoplastic breast-conserving surgery or a mastectomy with or without immediate breast reconstruction to explore their rationale for procedure choice. Interviews were transcribed verbatim and analysed thematically. Trial registration number: ISRCTN18238549.

Results
A total of 27 women from 12 centres were interviewed. Out of these, 12 had chosen oncoplastic breast-conserving surgery and 15 had chosen a mastectomy with or without immediate breast reconstruction. Overwhelmingly, women's decisions were guided by their surgical teams. Decision-making for and against oncoplastic breast-conserving surgery was influenced by three key inter-related factors: perceptions of oncological safety; the importance of maintaining/restoring femininity and body image; and practical issues. Oncological safety was paramount. Women who reported feeling reassured that oncoplastic breast-conserving surgery was oncologically safe were happy to choose this option. Those who were not reassured were more likely to opt for a mastectomy, as a perceived ‘safer’ option. Most women wished to maintain/restore femininity, with the offer of immediate breast reconstruction essential to make a mastectomy an acceptable option. Practical issues such as the perceived magnitude of the surgery were a lesser concern.

Conclusion
Decision-making is complex and heavily influenced by the surgical team. High-quality, accurate information about surgical options, including appropriate reassurance about the short- and long-term oncological safety of oncoplastic breast-conserving surgery is vital if women are to make fully informed decisions.
The relevance of Spearman's g for epilepsy
Authors: Struck Aaron F , Garcia-Ramos Camille , Nair Veena A , Prabhakaran Vivek , Dabbs Kevin , Conant Lisa L , Binder Jeffrey R , Loring David , Meyerand Mary , Hermann Bruce P 
Published: June 2024

Abstract
Whilst the concept of a general mental factor known as ‘g’ has been of longstanding interest, for unknown reasons, it has never been interrogated in epilepsy despite the 100+ year empirical history of the neuropsychology of epilepsy. This investigation seeks to identify g within a comprehensive neuropsychological data set and compare participants with temporal lobe epilepsy to controls, characterize the discriminatory power of g compared with domain-specific cognitive metrics, explore the association of g with clinical epilepsy and sociodemographic variables and identify the structural and network properties associated with g in epilepsy. Participants included 110 temporal lobe epilepsy patients and 79 healthy controls between the ages of 19 and 60. Participants underwent neuropsychological assessment, clinical interview and structural and functional imaging. Cognitive data were subjected to factor analysis to identify g and compare the group of patients with control participants. The relative power of g compared with domain-specific tests was interrogated, clinical and sociodemographic variables were examined for their relationship with g, and structural and functional images were assessed using traditional regional volumetrics, cortical surface features and network analytics. Findings indicate (i) significantly (P &lt; 0.005) lower g in patients compared with controls; (ii) g is at least as powerful as individual cognitive domain-specific metrics and other analytic approaches to discriminating patients from control participants; (iii) lower g was associated with earlier age of onset and medication use, greater number of antiseizure medications and longer epilepsy duration (Ps &lt; 0.04); and lower parental and personal education and greater neighbourhood deprivation (Ps &lt; 0.012); and (iv) amongst patients, lower g was linked to decreased total intracranial volume (P = 0.019), age and intracranial volume adjusted total tissue volume (P = 0.019) and age and intracranial volume adjusted total corpus callosum volume (P = 0.012)—particularly posterior, mid-posterior and anterior (Ps &lt; 0.022) regions. Cortical vertex analyses showed lower g to be associated specifically with decreased gyrification in bilateral medial orbitofrontal regions. Network analysis of resting-state data with focus on the participation coefficient showed g to be associated with the superior parietal network. Spearman's g is reduced in patients, has considerable discriminatory power compared with domain-specific metrics and is linked to a multiplex of factors related to brain (size, connectivity and frontoparietal networks), environment (familial and personal education and neighbourhood disadvantage) and disease (epilepsy onset, treatment and duration). Greater attention to contemporary models of human cognition is warranted in order to advance the neuropsychology of epilepsy.
Remote symptom monitoring with patient-reported outcome measures in outpatients with chronic kidney disease (PROKID): a multicentre randomised controlled non-inferiority study
Authors: Grove Birgith Engelst , Schougaard Liv Marit Valen , Mose Frank , Randers Else , Hjollund Niels Henrik , Ivarsen Per , De Thurah Annette 
Published: June 2024

ABSTRACT

Background
The increasing incidence of chronic kidney disease (CKD) is straining the capacity of outpatient clinics. Remote healthcare delivery might improve CKD follow-up compared with conventional face-to-face follow-up. Patient-reported outcomes (PROs) are used to empower remote follow-up and patient engagement. The consequences of shifting from face-to-face follow-up to remote outpatient follow-up on kidney function, health resource utilisation and quality of life remain unknown.

Methods
We conducted a multicentre pragmatic non-inferiority trial at three outpatient clinics in the Central Denmark Region. A total of 152 incident outpatients with CKD were randomised (1:1:1) to either PRO-based, PRO-telephone follow-up or standard of care (SoC). The primary outcome was the annual change in kidney function measured by the slope of the estimated glomerular filtration rate (eGFR). The non-inferiority margin was an eGFR of 2.85 ml/min/1.73 m2/year. Mean differences were estimated using intention-to-treat (ITT), per protocol and random coefficient models.

Results
Mean eGFR slope differences between PRO-based and SoC were −0.97 ml/min/1.73 m2/year [95% confidence interval (CI) −3.00–1.07] and −1.06 ml/min/1.73 m2/year (95% CI −3.02–0.89) between PRO-telephone and SoC. Non-inferiority was only established in the per-protocol analysis due to CIs exceeding the margin in the ITT group. Both intervention groups had fewer outpatient visits: −4.95 (95% CI −5.82 to −4.08) for the PRO-based group and −5.21 (95% CI −5.95 to −4.46) for the PRO-telephone group. We found no significant differences in quality of life, illness perception or satisfaction.

Conclusion
Differences in the eGFR slope between groups were non-significant and results on non-inferiority were inconclusive. Thus, transitioning to remote PRO-based follow-up requires close monitoring of kidney function. Reducing patients’ attendance in the outpatient clinic was possible without decreasing either quality of life or illness perception.
ClinicalTrials.gov identifier: NCT03847766
Impact of Prior Biologic or Janus Kinase Inhibitor Therapy on Efficacy and Safety of Etrasimod in the ELEVATE UC 52 and ELEVATE UC 12 Trials
Authors: Vermeire Séverine , Sands Bruce E , Peyrin-Biroulet Laurent , D’Haens Geert R , Panés Julian , Yarur Andres J , Wolf Douglas C , Ritter Timothy , Schreiber Stefan , Woolcott John C , Modesto Irene , Keating Michael , Shan Kevin , Wu Joseph , Chiorean Michael V , Baert Filip , Dubinsky Marla C , Goetsch Martina , Danese Silvio , Feagan Brian G 
Published: June 2024

Abstract

Background and Aims
Etrasimod is an oral, once daily, selective, sphingosine 1-phosphate [S1P]1,4,5 receptor modulator for the treatment of moderately to severely active ulcerative colitis [UC]. This subgroup analysis evaluated the efficacy and safety of etrasimod 2 mg once daily vs placebo by prior biologic/Janus kinase inhibitor [bio/JAKi] exposure in ELEVATE UC 52 and ELEVATE UC 12.

Methods
Pre-defined efficacy endpoints were assessed at Weeks 12 and 52 in ELEVATE UC 52 and Week 12 in ELEVATE UC 12 in bio/JAKi-naïve and -experienced patients, and at Week 12 [pooled] based on prior advanced therapy exposure mechanism.

Results
In the ELEVATE UC 52 and ELEVATE UC 12 analysis populations, 80/274 [29.2%] and 74/222 [33.3%] patients receiving etrasimod and 42/135 [31.1%] and 38/112 [33.9%] patients receiving placebo, respectively, were bio/JAKi-experienced. In both bio/JAKi-naïve and -experienced patients, a significantly greater proportion receiving etrasimod vs placebo achieved clinical remission [p &lt; 0.05] in ELEVATE UC 52 at Weeks 12 [naïve: 30.9% vs 9.7%; experienced: 17.5% vs 2.4%] and 52 [naïve: 36.6% vs 7.5%; experienced: 21.3% vs 4.8%]; in ELEVATE UC 12, this was observed only for bio/JAKi-naïve patients [naïve: 27.7% vs 16.2%, p = 0.033; experienced: 18.9% vs 13.2%, p = 0.349]. Similar patterns were observed for most efficacy endpoints. Among patients with prior anti-integrin exposure [N = 90], a significantly greater proportion achieved clinical response [54.1% vs 27.6%, p = 0.030], but not clinical remission [9.8% vs 3.4%, p = 0.248], with etrasimod vs placebo.

Conclusions
Bio/JAKi-naïve and -experienced patients had clinically meaningful induction and maintenance treatment benefits with etrasimod vs placebo.

ClinicalTrials.gov
NCT03945188; NCT03996369
Perioperative Enhanced Recovery Concepts Significantly Improve Postoperative Outcome in Patients with Crohn`s Disease
Authors: Kelm Matthias , Wagner Lena , Widder Anna , Pistorius Regina , Wagner Johanna C , Schlegel Nicolas , Markus Christian , Meybohm Patrick , Germer Christoph-Thomas , Schwenk Wolfgang , Flemming Sven 
Published: June 2024

Abstract

Background and Aims
Despite recent advancements in medical and surgical techniques in patients suffering from Crohn`s disease [CD], postoperative morbidity remains relevant due to a long-standing, non-curable disease burden. As demonstrated for oncological patients, perioperative enhanced recovery concepts provide great potential to improve postoperative outcome. However, robust evidence about the effect of perioperative enhanced recovery concepts in the specific cohort of CD patients is lacking.

Methods
In a prospective, single-centre study, all patients receiving ileocaecal resection due to CD between 2020 and 2023 were included. A specific, perioperative, enhanced recovery concept [ERC] was implemented and patients were divided into two groups [before and after implementation]. The primary outcome focused on postoperative complications as measured by the Comprehensive Complication Index [CCI], secondary endpoints were severe complications, length of hospital stay, and rates of re-admission.

Results
Of 83 patients analysed, 33 patients participated in the enhanced recovery programme [post-ERC]. Whereas patient characteristics were comparable between both groups, ERC resulted in significantly decreased rates of overall and severe postoperative complications [CCI: 21.4 versus 8.4, p = 0.0036; Clavien Dindo &gt; 2: 38% versus 3.1%, p = 0.0002]. Additionally, post-ERC-patients were ready earlier for discharge [5 days versus 6.5 days, p = 0.001] and rates of re-admission were significantly lower [3.1% versus 20%, p = 0.03]. In a multivariate analysis, the recovery concept was identified as independent factor to reduce severe postoperative complications [p = 0.019].

Conclusion
A specific, perioperative, enhanced recovery concept significantly improves the postoperative outcome of patients suffering from Crohn`s disease.
Intravenous Albumin Infusion Does not Augment the Response Rate to a Combination of Exclusive Enteral Nutrition and Intravenous Steroids in Acute Severe Ulcerative Colitis: A Randomised Controlled Trial
Authors: Mundhra Sandeep K , Madan Divya , Golla Rithvik , Sahu Pabitra , Vuyyuru Sudheer K , Kante Bhaskar , Kumar Peeyush , Mathew Thomas David , Prasad Shubham , Vaishnav Manas , Verma Mahak , Virmani Shubi , Bajaj Aditya , Markandey Manasvani , Ranjan Mukesh Kumar , Arora Umang , Singh Mukesh Kumar , Makharia Govind K , Ahuja Vineet , Kedia Saurabh 
Published: June 2024

Abstract

Introduction
Overall, 30–40% patients with acute severe ulcerative colitis [ASUC] fail intravenous [IV] steroids, requiring medical rescue therapy/colectomy. Low baseline albumin predicts steroid non-response, and exclusive enteral nutrition [EEN] has been shown to improve steroid response and albumin levels. Albumin infusion, due to its anti-inflammatory and antioxidant properties, might further improve steroid response in ASUC, which was evaluated in the present study.

Methods
In this open-label, randomised, controlled trial, patients with ASUC were randomised in 1:1 ratio to either albumin + standard of care [SOC] + EEN [Albumin arm] or SOC + EEN [SOC arm], over January 2021–February 2023. Both arms received 5 days of EEN with 400 mg IV hydrocortisone/day. Patients in the Albumin arm were administered 5 days of 20% weight/volume [w/v] intravenous albumin [100 ml]. Primary outcome was first, steroid failure [need for rescue medical therapy or colectomy] and second, proportion of patients with adverse events.

Results
In all, 61 patients [albumin: 30, SOC: 31][mean age 31.6 ± 0.4 years, male 57.4%], were included. Baseline characteristics were comparable. There was no difference in steroid failure between Albumin and SOC arms (10/30 [33.33%] vs 13/31[41.94%], p = 0.49). No adverse events were reported with albumin infusions. Colectomy rate [10% vs 9.68%, p = 1], response to salvage medical therapy [88.89% vs 76.92%, p = 0.62] and median [interquartile range] duration of hospitalisation [10.5 [7-16] vs 10 [7-20], p = 0.43] were also comparable. The long-term composite outcome of colectomy and re-admission rates was numerically higher in the Albumin than the SOC arm [37.04% vs 17.86%, p &gt; 0.05], although this did not reach statistical significance.

Conclusion
There was no benefit of intravenous albumin infusion as an adjunct to IV steroids and EEN in patients with ASUC.
Perinatal depression and risk of maternal cardiovascular disease: a Swedish nationwide study
Authors: Lu Donghao , Valdimarsdóttir Unnur A , Wei Dang , Chen Yufeng , Andreassen Ole A , Fang Fang , László Krisztina D , Bränn Emma 
Published: June 2024

Abstract

Background and Aims
Increasing evidence suggests that some reproductive factors/hazards are associated with a future risk of cardiovascular disease (CVD) in women. While major (non-perinatal) depression has consistently been associated with CVD, the long-term risk of CVD after perinatal depression (PND) is largely unknown.

Methods
A nationwide population-based matched cohort study involving 55 539 women diagnosed with PND during 2001–14 in Sweden and 545 567 unaffected women individually matched on age and year of conception/delivery was conducted. All women were followed up to 2020. Perinatal depression and CVD were identified from Swedish national health registers. Using multivariable Cox models, hazard ratios (HR) of any and type-specific CVD according to PND were estimated.

Results
The mean age at the PND diagnosis was 30.8 [standard deviation (SD) 5.6] years. During the follow-up of up to 20 years (mean 10.4, SD 3.6), 3533 (6.4%) women with PND (expected number 2077) and 20 202 (3.7%) unaffected women developed CVD. Compared with matched unaffected women, women with PND had a 36% higher risk of developing CVD [adjusted HR = 1.36, 95% confidence interval (CI): 1.31–1.42], while compared with their sisters, women with PND had a 20% higher risk of CVD (adjusted HR = 1.20, 95% CI 1.07–1.34). The results were most pronounced in women without a history of psychiatric disorder (P for interaction &lt; .001). The association was observed for all CVD subtypes, with the highest HR in the case of hypertensive disease (HR = 1.50, 95% CI: 1.41–1.60), ischaemic heart disease (HR = 1.37, 95% CI: 1.13–1.65), and heart failure (HR 1.36, 95% CI: 1.06–1.74).

Conclusions
Women with PND are at higher risk of CVD in middle adulthood. Reproductive history, including PND, should be considered in CVD risk assessments of women.
High potential but little success: ungulate browsing increasingly impairs silver fir regeneration in mountain forests in the southern Swiss Alps
Authors: Frei Esther R , Conedera Marco , Bebi Peter , Zürcher Samuel , Bareiss Alena , Ramstein Laura , Giacomelli Nicola , Bottero Alessandra 
Published: June 2024

Abstract
Sustainable regeneration of silver fir (Abies alba Mill.) is important for maintaining and improving the future resilience and protective capacity of mountain forests in the southern Swiss Alps. However, increasing densities of wild ungulates, such as red and roe deer, can hamper the regeneration success of silver fir. A comprehensive understanding of forest–wildlife interactions is essential to plan concrete measures for improving the adaptation potential of mountain forests. Here, we monitored the dynamics of natural silver fir regeneration in mountain protective forests. This study encompassed 30 unfenced permanent plots across two sites, Lostallo and Soazza, located in Valle Mesolcina in the southern Swiss Alps. These sites were selected for their comparable ecological characteristics related to silver fir regeneration, yet contrasting densities of mature, seed-bearing silver fir trees. We recorded the number of seedlings (&lt;10 cm height) and saplings (10–200 cm height), and repeatedly assessed height growth, frequency, and intensity of ungulate browsing on saplings in the summers 2016, 2019, and 2022. In 2022, we additionally recorded the presence of browsing on other tree species in the unfenced plots and the height growth increments of silver fir saplings in pre-existing fences. On average, 509 silver fir seedlings/ha were present in the study area, but there was a lower density of saplings (382 saplings/ha). Between 2016 and 2022, the browsing frequency on silver fir saplings increased from 33 per cent to nearly 100 per cent, accompanied by a significant rise in browsing intensity. Furthermore, sapling height growth from 2019 to 2022 was significantly reduced or even negative in the unfenced plots as compared to the growth of saplings in the fenced plots. The observed seedling density indicated a good potential for natural regeneration of silver fir, irrespective of the differences in the density of seed-bearing trees between the two sites. However, the increased ungulate browsing impaired successful regeneration in the considered mountain forests in the southern Swiss Alps. Thus, without an effective control of ungulate browsing, silver fir may not be able to substantially contribute to the transition to more resilient and future-proof mountain forests.
Tight General Bounds for the Extremal Numbers of 0–1 Matrices
Authors: Janzer Barnabás , Janzer Oliver , Magnan Van , Methuku Abhishek 
Published: June 2024

Abstract
A zero-one matrix $M$ is said to contain another zero-one matrix $A$ if we can delete some rows and columns of $M$ and replace some $1$-entries with $0$-entries such that the resulting matrix is $A$. The extremal number of $A$, denoted $\operatorname{ex}(n,A)$, is the maximum number of $1$-entries that an $n\times n$ zero-one matrix can have without containing $A$. The systematic study of this function for various patterns $A$ goes back to the work of Füredi and Hajnal from 1992, and the field has many connections to other areas of mathematics and theoretical computer science. The problem has been particularly extensively studied for so-called acyclic matrices, but very little is known about the general case (i.e., the case where $A$ is not necessarily acyclic). We prove the first asymptotically tight general result by showing that if $A$ has at most $t$ $1$-entries in every row, then $\operatorname{ex}(n,A)\leq n^{2-1/t+o(1)}$. This verifies a conjecture of Methuku and Tomon. Our result also provides the first tight general bound for the extremal number of vertex-ordered graphs with interval chromatic number $2$, generalizing a celebrated result of Füredi and Alon, Krivelevich, and Sudakov about the (unordered) extremal number of bipartite graphs with maximum degree $t$ in one of the vertex classes.