bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ninety-day hospital costs associated with prolonged air leak following lung resection
Authors: Brunelli Alessandro , Chapman Kath , Pompili Cecilia , Chaudhuri Nilanjan , Kefaloyannis Emmanuel , Milton Richard , Tcherveniakov Peter , Papagiannopoulos Kostas , Mitchell Thomas , Bassi Vinod 
Published: July 2020

Abstract

OBJECTIVES
Our goal was to assess the postoperative 90-day hospital costs of patients with prolonged air leak (PAL) including costs incurred after discharge from the initial index hospitalization.

METHODS
We performed a retrospective analysis of 982 patients undergoing lobectomy (898) or segmentectomy (78) (April 2014–August 2018). A total of 167 operations were open, 780 were video-assisted thoracoscopic surgery and 28 were robotic. A PAL was defined as an air leak &gt;5 days. The 90-day postoperative costs included all fixed and variable costs incurred during the 90 days following surgery. The postoperative costs of patients with and without PAL were compared. The independent association of PAL with postoperative 90-day costs was tested after adjustment for patient-related factors and other complications by a multivariable regression analysis.

RESULTS
PAL occurred in 261 patients (27%). Their postoperative stay was 4 days longer than that of those without PAL (9.6 vs 5.7; P &lt; 0.0001). Compared to patients without PAL, those with PAL had 27% higher index postoperative costs [7354€, standard deviation (SD) 7646 vs 5759€, SD 7183, P &lt; 0.0001] and 40% higher 90-day postoperative costs (18 340€, SD 23 312 vs 13 102€, SD 10 264; P &lt; 0.0001). The relative postoperative costs (the difference between 90-day and index postoperative costs) were 50% higher in PAL patients compared to non-PAL patients (P &lt; 0.0001) and accounted for 60% of the total 90-day costs. Multivariable regression analysis showed that PAL remained an independent factor associated with 90-day costs (P &lt; 0.0001) along with the occurrence of other cardiopulmonary complications (P &lt; 0.0001), male gender (P = 0.018), low carbon monoxide lung diffusion capacity (P = 0.043) and thoracotomy approach (P = 0.022).

CONCLUSIONS
PAL is associated not only with increased index hospitalization costs but also with increased costs after discharge. Evaluation of the cost-effectiveness of measures to prevent air leaks should also include post-discharge costs.
Quantitative stability and error estimates for optimal transport plans
Authors: Li Wenbo , Nochetto Ricardo H 
Published: July 2020

Abstract
Optimal transport maps and plans between two absolutely continuous measures $\mu$ and $\nu$ can be approximated by solving semidiscrete or fully discrete optimal transport problems. These two problems ensue from approximating $\mu$ or both $\mu$ and $\nu$ by Dirac measures. Extending an idea from Gigli (2011, On Hölder continuity-in-time of the optimal transport map towards measures along a curve. Proc. Edinb. Math. Soc. (2), 54, 401–409), we characterize how transport plans change under the perturbation of both $\mu$ and $\nu$. We apply this insight to prove error estimates for semidiscrete and fully discrete algorithms in terms of errors solely arising from approximating measures. We obtain weighted $L^2$ error estimates for both types of algorithms with a convergence rate $O(h^{1/2})$. This coincides with the rate in Theorem 5.4 in Berman (2018, Convergence rates for discretized Monge–Ampère equations and quantitative stability of optimal transport. Preprint available at arXiv:1803.00785) for semidiscrete methods, but the error notion is different.
Conditional Expectation, Entropy, and Transport for Convex Gibbs Laws in Free Probability
Authors: Jekel David 
Published: July 2020

Abstract
Let $(X_1,\dots ,X_m)$ be self-adjoint noncommutative random variables distributed according to the free Gibbs law given by a sufficiently regular convex and semi-concave potential $V$, and let $(S_1,\dots ,S_m)$ be a free semicircular family. For $k &lt; m$, we show that conditional expectations and conditional non-microstates free entropy given $X_1$, …, $X_k$ arise as the large $N$ limit of the corresponding conditional expectations and entropy for the $N \times N$ random matrix models associated to $V$. Then, by studying conditional transport of measure for the matrix models, we construct an isomorphism $\mathrm{W}^*(X_1,\dots ,X_m) \to \mathrm{W}^*(S_1,\dots ,S_m)$ that maps $\mathrm{W}^*(X_1,\dots ,X_k)$ to $\mathrm{W}^*(S_1,\dots ,S_k)$ for each $k = 1, \dots , m$ and that also witnesses the Talagrand inequality for the law of $(X_1,\dots ,X_m)$ relative to the law of $(S_1,\dots ,S_m)$.
Studies on the role of IS1216E in the formation and dissemination of poxtA-carrying plasmids in an Enterococcus faecium clade A1 isolate
Authors: Shan Xinxin , Li Xin-Sheng , Wang Nannan , Schwarz Stefan , Zhang Su-Mei , Li Dexi , Du Xiang-Dang 
Published: July 2020

Abstract

Objectives
To analyse the role of IS1216E in the dissemination of the phenicol-oxazolidinone-tetracycline resistance gene poxtA in an Enterococcus faecium clade A1 isolate.

Methods
MICs were determined by broth microdilution. The poxtA-positive isolate was typed by MLST. The two plasmids were characterized by PCR, conjugation, S1-PFGE, Southern blot hybridization and WGS analysis. The presence of translocatable units (TUs) was examined by PCR and sequencing.

Results
Isolate E1077 contains the 217661 bp conjugative plasmid pE1077-217 and the 23710 bp mobilizable plasmid pE1077-23. pE1077-217 harbours erm(B), aac(A)-aph(D), aadE, spw, lsa(E), lnu(B), aphA3 and dfrG, whereas pE1077-23 carries a Tn6657-like transposon containing poxtA and fexB. pE1077-23 was apparently formed by an IS1216E-mediated composite transposon–plasmid fusion event, involving a replicative transposition process. Conjugation experiments showed that pE1077-23 is mobilizable by pE1077-217. Moreover, a novel 31742 bp plasmid, pT-E1077-31, was found in a transconjugant. WGS analysis indicated that pT-E1077-31 was formed by the integration of a Tn6657-derived, IS1216E-based translocatable unit, which carried fexB and poxtA, into a copy of pE1077-23.

Conclusions
This study showed the presence of two cointegrate formation events in the formation and spread of a poxtA/fexB-carrying plasmid in E. faecium. One was the integration of a transposon into a plasmid while the other was the integration of a TU into a different site of the same type of plasmid-borne transposon from which it originated. In both events, IS1216E played a major role, suggesting that IS1216E-mediated transposition and translocation processes aid the dissemination and persistence of important antimicrobial resistance genes, such as poxtA, among enterococci.
Cross-lingual Unified Medical Language System entity linking in online health communities
Authors: Bitton Yonatan , Cohen Raphael , Schifter Tamar , Bachmat Eitan , Elhadad Michael , Elhadad Noémie 
Published: July 2020

Abstract

Objective
In Hebrew online health communities, participants commonly write medical terms that appear as transliterated forms of a source term in English. Such transliterations introduce high variability in text and challenge text-analytics methods. To reduce their variability, medical terms must be normalized, such as linking them to Unified Medical Language System (UMLS) concepts. We present a method to identify both transliterated and translated Hebrew medical terms and link them with UMLS entities.

Materials and Methods
We investigate the effect of linking terms in Camoni, a popular Israeli online health community in Hebrew. Our method, MDTEL (Medical Deep Transliteration Entity Linking), includes (1) an attention-based recurrent neural network encoder-decoder to transliterate words and mapping UMLS from English to Hebrew, (2) an unsupervised method for creating a transliteration dataset in any language without manually labeled data, and (3) an efficient way to identify and link medical entities in the Hebrew corpus to UMLS concepts, by producing a high-recall list of candidate medical terms in the corpus, and then filtering the candidates to relevant medical terms.

Results
We carry out experiments on 3 disease-specific communities: diabetes, multiple sclerosis, and depression. MDTEL tagging and normalizing on Camoni posts achieved 99% accuracy, 92% recall, and 87% precision. When tagging and normalizing terms in queries from the Camoni search logs, UMLS-normalized queries improved search results in 46% of the cases.

Conclusions
Cross-lingual UMLS entity linking from Hebrew is possible and improves search performance across communities. Annotated datasets, annotation guidelines, and code are made available online (https://github.com/yonatanbitton/mdtel).
Developmental and hormonal regulation of ubiquitin-like with plant homeodomain and really interesting new gene finger domains 1 gene expression in ovarian granulosa and theca cells of cattle
Authors: Perego Maria Chiara , Morrell Breanne C , Zhang Lingna , Schütz Luis F , Spicer Leon J 
Published: July 2020

Abstract
Ubiquitin-like with plant homeodomain and really interesting new gene finger domains 1 (UHRF1) is a multi-domain nuclear protein that plays an important role in epigenetics and tumorigenesis, but its role in normal ovarian follicle development remains unknown. Thus, the present study evaluated if UHRF1 mRNA abundance in bovine follicular cells is developmentally and hormonally regulated, and if changes in UHRF1 are associated with changes in DNA methylation in follicular cells. Abundance of UHRF1 mRNA was greater in granulosa cells (GC) and theca cells (TC) from small (&lt;6 mm) than large (≥8 mm) follicles and was greater in small-follicle GC than TC. In GC and TC, fibroblast growth factor 9 (FGF9) treatment increased (P &lt; 0.05) UHRF1 expression by 2-fold. Also, luteinizing hormone (LH) and insulin-like growth factor 1 (IGF1) increased (P &lt; 0.05) UHRF1 expression in TC by 2-fold, and forskolin (an adenylate cyclase inducer) alone or combined with IGF1 increased (P &lt; 0.05) UHRF1 expression by 3-fold. An E2F transcription factor inhibitor (E2Fi) decreased (P &lt; 0.05) UHRF1 expression by 44% in TC and by 99% in GC. Estradiol, progesterone, and dibutyryl-cAMP decreased (P &lt; 0.05) UHRF1 mRNA abundance in GC. Treatment of GC with follicle-stimulating hormone (FSH) alone had no effect but when combined with IGF1 enhanced the UHRF1 mRNA abundance by 2.7-fold. Beauvericin (a mycotoxin) completely inhibited the FSH plus IGF1-induced UHRF1 expression in small-follicle GC. Treatments that increased UHRF1 mRNA (i.e., FGF9) in GC tended to decrease (by 63%; P &lt; 0.10) global DNA methylation, and those that decreased UHRF1 mRNA (i.e., E2Fi) in GC tended to increase (by 2.4-fold; P &lt; 0.10) global DNA methylation. Collectively, these results suggest that UHRF1 expression in both GC and TC is developmentally and hormonally regulated, and that UHRF1 may play a role in follicular growth and development as well as be involved in ovarian epigenetic processes.
Enzymatic Debridement of Porcine Burn Wounds via a Novel Protease, SN514
Authors: Stone Randolph , Jockheck-Clark Angela R , Natesan Shanmugasundaram , Rizzo Julie A , Wienandt Nathan A , Scott Laura L , Larson David A , Wall John T , Holik Michelle A , Shaffer Lucy J , Park Nancy , Jovanovic Aleksa , Tetens Shannon , Roche Eric D , Shi Lei , Christy Robert J 
Published: July 2020

Abstract
Necrotic tissue generated by a thermal injury is typically removed via surgical debridement. However, this procedure is commonly associated with blood loss and the removal of viable healthy tissue. For some patients and contexts such as extended care on the battlefield, it would be preferable to remove devitalized tissue with a nonsurgical debridement agent. In this paper, a proprietary debridement gel (SN514) was evaluated for the ability to debride both deep-partial thickness (DPT) and full-thickness burn wounds using an established porcine thermal injury model. Burn wounds were treated daily for 4 days and visualized with both digital imaging and laser speckle imaging. Strip biopsies were taken at the end of the procedure. Histological analyses confirmed a greater debridement of the porcine burn wounds by SN514 than the vehicle-treated controls. Laser speckle imaging detected significant increases in the perfusion status after 4 days of SN514 treatment on DPT wounds. Importantly, histological analyses and clinical observations suggest that SN514 gel treatment did not damage uninjured tissue as no edema, erythema, or inflammation was observed on intact skin surrounding the treated wounds. A blinded evaluation of the digital images by a burn surgeon indicated that SN514 debrided more necrotic tissue than the control groups after 1, 2, and 3 days of treatment. Additionally, SN514 gel was evaluated using an in vitro burn model that used human discarded skin. Treatment of human burned tissue with SN514 gel resulted in greater than 80% weight reduction compared with untreated samples. Together, these data demonstrate that SN514 gel is capable of debriding necrotic tissue and suggest that SN514 gel could be a useful option for austere conditions, such as military multi-domain operations and prolonged field care scenarios.
Difficulty in differential diagnosis for renal cancer with microscopic papillary architecture: overlapped pathological features among papillary renal cell carcinoma (RCC), mutinous tubular and spindle cell carcinoma, and unclassified RCC. Lessons from a Japanese multicenter study
Authors: Ito Keiichi , Mikami Shuji , Kuroda Naoto , Nagashima Yoji , Tatsugami Katsunori , Masumori Naoya , Kondo Tsunenori , Takagi Toshio , Nakanishi Shotaro , Eto Masatoshi , Kamba Tomomi , Tomita Yoshihiko , Matsuyama Hideyasu , Tsushima Tomoyasu , Nakazawa Hayakazu , Oya Mototsugu , Kimura Go , Shinohara Nobuo , Asano Tomohiko 
Published: July 2020

Abstract

Objectives
In our multicenter study evaluating metastatic papillary renal cell carcinoma (PRCC), 29% of tumors diagnosed as PRCC in collaborative institutes were finally diagnosed as other RCCs under central review. In those tumors, mucinous tubular and spindle cell carcinoma (MTSCC) was the leading histology, followed by unclassified RCC (ucRCC). We focused on those patients with MTSCC or ucRCC.

Methods
We reviewed the processes for the pathological diagnoses of nine tumors and reviewed their clinical features.

Results
All of the MTSCCs and ucRCCs were positive for AMACR, which is frequently positive in PRCC. Mucin was demonstrated in 80% of the MTSCCs, and its presence is important for their diagnoses. One MTSCC was diagnosed as a mucin-poor variant. The presence of spindle cells with low-grade nuclei was suggestive of MTSCC, but the diagnosis of high-grade MTSCC was difficult. Four tumors were diagnosed as ucRCC by histological and immunohistochemical findings. Three of the four tumors were suspicious of ucRCC in the initial review due to atypical findings as PRCC. Sunitinib and interferon-α were effective for one MTSCC patient who survived for &gt;5 years. Two MTSCC patients who were Memorial Sloan-Kettering Cancer Center poor risk had unfavorable prognoses. One patient with mucin-poor MTSCC had an indolent clinical course. Two of four ucRCC patients showed durable stable disease with targeted agents (TAs) and survived &gt;3 years.

Conclusion
Some MTSCC metastases progressed very slowly and poor-risk tumors progressed rapidly. Systemic therapies including TAs showed some efficacies. Some patients who have metastatic ucRCC with microscopic papillary architecture can benefit from TAs.
Mark–recapture of individually distinctive calls—a case study with signature whistles of bottlenose dolphins (Tursiops truncatus)
Authors: Longden Emma G , Elwen Simon H , McGovern Barry , James Bridget S , Embling Clare B , Gridley Tess 
Published: July 2020

Abstract
Robust abundance estimates of wild animal populations are needed to inform management policies and are often obtained through mark–recapture (MR) studies. Visual methods are commonly used, which limits data collection to daylight hours and good weather conditions. Passive acoustic monitoring offers an alternative, particularly if acoustic cues are naturally produced and individually distinctive. Here we investigate the potential of using individually distinctive signature whistles in a MR framework and evaluate different components of study design. We analyzed signature whistles of common bottlenose dolphins, Tursiops truncatus, using data collected from static acoustic monitoring devices deployed in Walvis Bay, Namibia. Signature whistle types (SWTs) were identified using a bout analysis approach (SIGnature IDentification [SIGID]—Janik et al. 2013). We investigated spatial variation in capture by comparing 21 synchronized recording days across four sites, and temporal variation from 125 recording days at one high-use site (Aphrodite Beach). Despite dolphin vocalizations (i.e., echolocation clicks) being detected at each site, SWTs were not detected at all sites and there was high variability in capture rates among sites where SWTs were detected (range 0–21 SWTs detected). At Aphrodite Beach, 53 SWTs were captured over 6 months and discovery curves showed an initial increase in newly detected SWTs, approaching asymptote during the fourth month. A Huggins closed capture model constructed from SWT capture histories at Aphrodite Beach estimated a population of 54–68 individuals from acoustic detection, which overlaps with the known population size (54–76 individuals—Elwen et al. 2019). This study demonstrates the potential power of using signature whistles as proxies for individual occurrence and in MR abundance estimation, but also highlights challenges in using this approach.
Travellers with type 1 diabetes: questionnaire development and descriptive analysis of knowledge and practices
Authors: Flaherty Gerard T , Leong Shan Wei , Finn Yvonne , Sulaiman Lokman Hakim , Noone Chris 
Published: July 2020

Abstract

Background
Little is known about the awareness of travellers with diabetes about the health effects of international travel. This study aimed to design and validate a questionnaire to examine the travel health knowledge, attitudes and practices of people living with type 1 diabetes.

Methods
A set of 74 items based on a conceptual framework analysis underwent revision and its content validity was established. Items were grouped into three domains. A development study was conducted to establish evidence regarding their factorial structure. A construct validation study was then conducted in which the retained items were tested in an independent sample using confirmatory factor analysis (CFA).

Results
Four factors emerged from our development study and were labelled as pre-travel preparation—insect bites, pre-travel preparation—consultation, insulin and glycaemic control and travel risk behaviour. A CFA confirmed the factorial structure identified in the development study in an independent sample. Each factor loading had a significant (P &lt; 0.001) loading of at least 0.4. The factor correlations ranged between 0.1 and 0.6, indicating good discriminant validity. The highest mean domain score in our sample of 268 participants related to insulin and glycaemic control (6.45), followed by travel risk behaviour (5.21) and pre-travel preparation (4.15).

Conclusions
This valid questionnaire for measuring the degree of preparedness of travellers with type 1 diabetes may prove a useful tool in studies involving travellers with type1 diabetes. Our results suggest that improvements are needed in relation to timely pre-travel consultation and screening for diabetic complications.
The past history of galaxy clusters told by their present neighbours
Authors: Sorce Jenny G , Gottlöber Stefan , Yepes Gustavo 
Published: July 2020

ABSTRACT
Galaxy clusters can play a key role in modern cosmology, provided their evolution is properly understood. However, observed clusters give us only a single timeframe of their dynamical state. Therefore, finding present observable data of clusters that are well correlated to their assembly history constitutes an inestimable tool for cosmology. Former studies correlating environmental descriptors of clusters to their formation history are dominated by halo mass–environment relations. This paper presents a mass-free correlation between the present neighbour distribution of cluster-size haloes and the latter mass assembly history. From the Big Multidark simulation, we extract two large samples of random haloes with masses ranging from Virgo to Coma cluster sizes. Additionally, to find the main environmental culprit for the formation history of the Virgo cluster, we compare the Virgo-size haloes to 200 Virgo-like haloes extracted from simulations that resemble the local Universe. The number of neighbours at different cluster-centric distances permits discriminating between clusters with different mass accretion histories. Similarly to Virgo-like haloes, clusters with numerous neighbours within a distance of about two times their virial radius experience a transition at z ≈ 1 between an active period of mass accretion, relative to the mean, and a quiet history. In contrary, clusters with few neighbours share an opposite trend: from passive to active assembly histories. Additionally, clusters with massive companions within about four times their virial radius tend to have recent active merging histories. Therefore, the radial distribution of cluster neighbours provides invaluable insights into the past history of these objects.
Diffusion Tensor Imaging Tractography for Fornix Identification in Intraventricular Tumor Surgery: A Case Series
Authors: Milton Camille K , Palejwala Ali H , O'Connor Kyle P , McCoy Tressie M , Conner Andrew K , Glenn Chad A 
Published: July 2020

ABSTRACT

BACKGROUND
The proximity of intraventricular or periventricular tumors to critical white matter structures, such as the fornix, poses an operative challenge. In order to avoid significant neurological morbidity, deliberate selection of surgical approach is necessary when planning resection of tumors in this region. We report our initial experience with fornix modeling as an adjunct to standard navigational techniques across multiple pathologies.

OBJECTIVE
To report the feasibility of using diffusion tensor imaging (DTI) fornix modeling as an adjunct to standard navigational techniques for surgical treatment of intraventricular and periventricular tumors involving the fornix.

METHODS
Between July 2018 and August 2019, DTI tractography was performed on 12 patients with intraventricular or periventricular tumors involving the fornix. DTI fornix modeling was performed and included as part of the intraoperative navigation in all cases.

RESULTS
The patient group was composed of 6 males and 6 females. The fornix model was delineated in all cases using DTI tractography as described. The mean patient age was 45.7 yr. The 2 most-common tumor pathologies represented in our patient cohort included meningioma and cranipharyngioma, both found in 2 patients. A glioneuronal tumor, low-grade glioma, ependymoma, subependymoma, mixed germ-cell tumor, pituitary adenoma, and renal cell carcinoma metastasis were found in 1 patient each. Case examples of fornix modeling that may be incorporated into standard neuronavigation are presented. No patient experienced new or worsening post-operative memory deficits.

CONCLUSION
DTI tractography for fornix identification is a useful adjunct to standard navigational techniques employed in surgical resection of forniceal involving tumors.