bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracting individual trees from lidar point clouds using treeseg
Authors: Burt Andrew , Disney Mathias , Calders Kim 
Published: November 2018

Abstract

Recent studies have demonstrated the potential of lidar‐derived methods in plant ecology and forestry. One limitation to these methods is accessing the information content of point clouds, from which tree‐scale metrics can be retrieved. This is currently undertaken through laborious and time‐consuming manual segmentation of tree‐level point clouds from larger‐area point clouds, an effort that is impracticable across thousands of stems.

Here, we present treeseg, an open‐source software to automate this task. This method utilises generic point cloud processing techniques including Euclidean clustering, principal component analysis, region‐based segmentation, shape fitting and connectivity testing. This data‐driven approach uses few a priori assumptions of tree architecture, and transferability across lidar instruments is constrained only by data quality requirements.

We demonstrate the treeseg algorithm here on data acquired from both a structurally simple open forest and a complex tropical forest. Across these data, we successfully automatically extract 96% and 70% of trees, respectively, with the remainder requiring some straightforward manual segmentation.

treeseg allows ready and quick access to tree‐scale information contained in lidar point clouds. treeseg should help contribute to more wide‐scale uptake of lidar‐derived methods to applications ranging from the estimation of carbon stocks through to descriptions of plant form and function.
Prospective Validation of a Checklist to Predict Short‐term Death in Older Patients After Emergency Department Admission in Australia and Ireland
Authors: Cardona Magnolia , O'Sullivan Michael , Lewis Ebony T. , Turner Robin M. , Garden Frances , Alkhouri Hatem , Asha Stephen , Mackenzie John , Perkins Margaret , Suri Sam , Holdgate Anna , Winoto Luis , Chang David C. W. , Gallego‐Luxan Blanca , McCarthy Sally , Hillman Ken , Breen Dorothy 
Published: November 2018

AbstractBackgroundEmergency departments (EDs) are pressured environment where patients with supportive and palliative care needs may not be identified. We aimed to test the predictive ability of the CriSTAL (Criteria for Screening and Triaging to Appropriate aLternative care) checklist to flag patients at risk of death within 3 months who may benefit from timely end‐of‐life discussions.MethodsProspective cohorts of >65‐year‐old patients admitted for at least one night via EDs in five Australian hospitals and one Irish hospital. Purpose‐trained nurses and medical students screened for frailty using two instruments concurrently and completed the other risk factors on the CriSTAL tool at admission. Postdischarge telephone follow‐up was used to determine survival status. Logistic regression and bootstrapping techniques were used to test the predictive accuracy of CriSTAL for death within 90 days of admission as primary outcome. Predictability of in‐hospital death was the secondary outcome.ResultsA total of 1,182 patients, with median age 76 to 80 years (IRE‐AUS), were included. The deceased had significantly higher mean CriSTAL with Australian mean of 8.1 (95% confidence interval [CI] = 7.7–8.6) versus 5.7 (95% CI = 5.1–6.2) and Irish mean of 7.7 (95% CI = 6.9–8.5) versus 5.7 (95% CI = 5.1–6.2). The model with Fried frailty score was optimal for the derivation (Australian) cohort but prediction with the Clinical Frailty Scale (CFS) was also good (areas under the receiver‐operating characteristic [AUROC] = 0.825 and 0.81, respectively). Values for the validation (Irish) cohort were AUROC = 0.70 with Fried and 0.77 using CFS. A minimum of five of 29 variables were sufficient for accurate prediction, and a cut point of 7+ or 6+ depending on the cohort was strongly indicative of risk of death. The most significant independent predictor of short‐term death in both cohorts was frailty, carrying a twofold risk of death. CriSTAL's accuracy for in‐hospital death prediction was also good (AUROC = 0.795 and 0.81 in Australia and Ireland, respectively), with high specificity and negative predictive values.ConclusionsThe modified CriSTAL tool (with CFS instead of Fried's frailty instrument) had good discriminant power to improve certainty of short‐term mortality prediction in both health systems. The predictive ability of models is anticipated to help clinicians gain confidence in initiating earlier end‐of‐life discussions. The practicalities of embedding screening for risk of death in routine practice warrant further investigation.
Identifying the optimal regional predictor of right ventricular global function: a high‐resolution three‐dimensional cardiac magnetic resonance study
Authors: Dawes T. J. W. , de Marvao A. , Shi W. , Rueckert D. , Cook S. A. , O'Regan D. P. 
Published: November 2018

SummaryRight ventricular (RV) function has prognostic value in acute, chronic and peri‐operative disease, although the complex RV contractile pattern makes rapid assessment difficult. Several two‐dimensional (2D) regional measures estimate RV function, however the optimal measure is not known. High‐resolution three‐dimensional (3D) cardiac magnetic resonance cine imaging was acquired in 300 healthy volunteers and a computational model of RV motion created. Points where regional function was significantly associated with global function were identified and a 2D, optimised single‐point marker (SPM‐O) of global function developed. This marker was prospectively compared with tricuspid annular plane systolic excursion (TAPSE), septum‐freewall displacement (SFD) and their fractional change (TAPSE‐F, SFD‐F) in a test cohort of 300 patients in the prediction of RV ejection fraction. RV ejection fraction was significantly associated with systolic function in a contiguous 7.3 cm2 patch of the basal RV freewall combining transverse (38%), longitudinal (35%) and circumferential (27%) contraction and coinciding with the four‐chamber view. In the test cohort, all single‐point surrogates correlated with RV ejection fraction (p < 0.010), but correlation (R) was higher for SPM‐O (R = 0.44, p < 0.001) than TAPSE (R = 0.24, p < 0.001) and SFD (R = 0.22, p < 0.001), and non‐significantly higher than TAPSE‐F (R = 0.40, p < 0.001) and SFD‐F (R = 0.43, p < 0.001). SPM‐O explained more of the observed variance in RV ejection fraction (19%) and predicted it more accurately than any other 2D marker (median error 2.8 ml vs 3.6 ml, p < 0.001). We conclude that systolic motion of the basal RV freewall predicts global function more accurately than other 2D estimators. However, no markers summarise 3D contractile patterns, limiting their predictive accuracy.
The early repolarization pattern: Echocardiographic characteristics in elite athletes
Authors: Reinhard Wibke , Trenkwalder Teresa , Haller Bernhard , Meindl Christine , Schoenfeld Julia , Kaess Bernhard M , Hengstenberg Christian , Schunkert Heribert , Pressler Axel , Halle Martin , Scherr Johannes 
Published: November 2018

AbstractBackgroundThe electrocardiographic early repolarization (ER) pattern is associated with idiopathic ventricular fibrillation and increased long‐term cardiovascular mortality. Whether structural cardiac aberrations influence the phenotype is unclear. Since ER is particularly common in athletes, we evaluated its prevalence and investigated predisposing echocardiographic characteristics and cardiopulmonary exercise capacity in a cohort of elite athletes.MethodsA total of 623 elite athletes (age 21 ± 5 years) were examined during annual preparticipation screening from 2006 until 2012 including electrocardiography, echocardiography, and exercise testing. ECGs were analyzed with focus on ER. All athletes participated in a clinical follow‐up.ResultsThe prevalence of ER was 17% (108/623). ER‐positive athletes were predominantly male (71%, 77/108), showed a lower heart rate (57.1 ± 9.3 bpm versus 60.0 ± 11.2 bpm; p = 0.015) and a higher lean body mass compared to ER‐negative participants (88.1% ± 5.6% versus 86.5% ± 6.3%; p = 0.015). Echocardiographic measurements and cardiopulmonary exercise capacity in male and female athletes with and without ER largely showed similar results. Only the notching ER subtype (n = 15) was associated with an increased left atrial diameter (OR 7.01, 95%CI 1.65–29.83; p = 0.008), a higher left ventricular mass (OR 1.02, 95%CI 1.00–1.03; p = 0.038) and larger relative heart volume (OR 1.01, 95%CI 1.00–1.01; p = 0.01). During a follow‐up of 7.4 ± 1.5 years, no severe cardiovascular event occurred in the study sample.ConclusionsIn elite athletes presence of ER is not associated with distinct alterations in echocardiography and cardiopulmonary exercise. Athletes presenting with ER are rather male, lean with a low heart rate.
Complete intracorporeal defect closure using unidirectional barbed suture in laparoscopic incisional hernia repair: Preliminary experience with short‐term follow‐up
Authors: Tsujinaka Shingo , Kakizawa Nao , Fukuda Rintaro , Kikugawa Rina , Toyama Nobuyuki , Rikiyama Toshiki 
Published: November 2018

AbstractIntroductionSurgical techniques to close defects in laparoscopic incisional hernia repair vary across the literature. We herein demonstrate our original and standardized surgical technique for laparoscopic incisional hernia repair with complete intracorporeal defect closure using barbed suture.Materials and Surgical TechniqueComplete intracorporeal defect closures were indicated for defects less than or equal to 6 cm in transverse diameter. We performed a defect closure with a running suture using barbed suture in a caudal to cranial direction, with tissue bites and inter‐suture spacing of 1 cm each. The hernial sac was incorporated into the suturing to reduce possible dead space. After the procedure, intraperitoneal onlay mesh was placed. Seven patients underwent this procedure. The median total operative time was 188 min, and the median time specifically for defect closure was 25 min. There was no seroma, mesh bulge, persisting pain, or hernia recurrence at follow‐up.DiscussionOur proposed technique is simple and can be safely performed with good short‐term outcomes.
Physiologically‐based pharmacokinetic modelling to predict oprozomib CYP3A drug–drug interaction potential in patients with advanced malignancies
Authors: Ou Ying , Xu Yang , Gore Lia , Harvey R. Donald , Mita Alain , Papadopoulos Kyriakos P. , Wang Zhengping , Cutler Richard E. , Pinchasik Dawn E. , Tsimberidou Apostolia M. 
Published: November 2018

AimsOprozomib is an oral, second‐generation, irreversible proteasome inhibitor currently in clinical development for haematologic malignancies, including multiple myeloma and other malignancies. Oprozomib is a rare example of a small molecule drug that demonstrates cytochrome P450 (CYP) mRNA suppression. This unusual property elicits uncertainty regarding the optimal approach for predicting its drug–drug interaction (DDI) risk. The current study aims to understand DDI potential during early clinical development of oprozomib.MethodsTo support early development of oprozomib (e.g. inclusion/exclusion criteria, combination study design), we used human hepatocyte data and physiologically‐based pharmacokinetic (PBPK) modelling to predict its CYP3A4‐mediated DDI potential. Subsequently, a clinical DDI study using midazolam as the substrate was conducted in patients with advanced malignancies.ResultsThe clinical DDI study enrolled a total of 21 patients, 18 with advanced solid tumours. No patient discontinued oprozomib due to a treatment‐related adverse event. The PBPK model prospectively predicted oprozomib 300 mg would not cause a clinically relevant change in exposure to CYP3A4 substrates (≤30%), which was confirmed by the results of this clinical DDI study.ConclusionsThese results indicate oprozomib has a low potential to inhibit the metabolism of CYP3A4 substrates in humans. The study shows that cultured human hepatocytes are a more reliable system for DDI prediction than human liver microsomes for studying this class of compounds. Developing a PBPK model prior to a clinical DDI study has been valuable in supporting clinical development of oprozomib.
Ex vivo culture of cells derived from circulating tumour cell xenograft to support small cell lung cancer research and experimental therapeutics
Authors: Lallo Alice , Gulati Sakshi , Schenk Maximilian W , Khandelwal Garima , Berglund Ulrika Warpman , Pateras Ioannis S , Chester Christopher P E , Pham Therese M , Kalderen Christina , Frese Kristopher K , Gorgoulis Vassilis G , Miller Crispin , Blackhall Fiona , Helleday Thomas , Dive Caroline 
Published: November 2018

Background and PurposeSmall cell lung cancer (SCLC) is an aggressive disease with median survival of <2 years. Tumour biopsies for research are scarce, especially from extensive‐stage patients, with repeat sampling at disease progression rarely performed. We overcame this limitation for relevant preclinical models by developing SCLC circulating tumour cell derived explants (CDX), which mimic the donor tumour pathology and chemotherapy response. To facilitate compound screening and identification of clinically relevant biomarkers, we developed short‐term ex vivo cultures of CDX tumour cells.Experimental ApproachCDX tumours were disaggregated, and the human tumour cells derived were cultured for a maximum of 5 weeks. Phenotypic, transcriptomic and pharmacological characterization of these cells was performed.Key ResultsCDX cultures maintained a neuroendocrine phenotype, and most changes in the expression of protein‐coding genes observed in cultures, for up to 4 weeks, were reversible when the cells were re‐implanted in vivo. Moreover, the CDX cultures exhibited a similar sensitivity to chemotherapy compared to the corresponding CDX tumour in vivo and were able to predict in vivo responses to therapeutic candidates.Conclusions and ImplicationsShort‐term cultures of CDX provide a tractable platform to screen new treatments, identify predictive and pharmacodynamic biomarkers and investigate mechanisms of resistance to better understand the progression of this recalcitrant tumour.
Science in support of Amazonian conservation in the 21st century: the case of Brazil
Authors: Simmons Cynthia S. , Famolare Lisa , Macedo Marcia N. , Walker Robert T. , Coe Michael T. , Scheffers Brett , Arima Eugenio , Munoz‐Carpena Rafael , Valle Denis , Fraisse Clyde , Moorcroft Paul , Diniz Marcelo , Diniz Marcia , Szlafsztein Claudio , Pereira Ritaumaria , Ruiz Cesar , Rocha Gilberto , Juhn Daniel , Otávio do Canto Lopes Luis , Waylen Michael , Antunes Aghane , Galvan Yankuic M 
Published: November 2018

AbstractThis article presents a 21st Century agenda for Amazonian conservation. The agenda calls for developing a system of refugia and a scientific methodology for predicting impacts of the infrastructure development vision for the region. It also calls for a collaborative approach to conservation planning, in the interest of fruitful engagement with decision‐makers and stakeholders. The ideas explored here emerged from the collaboration of peers over a decade, which culminated in a panel presentation, Scientific Analysis, and Simulation Models to Support Conservation and Development Decision‐Making, at the Tools and Strategies Workshop held at the University of Florida in October, 2017.
Methylchloroisothiazolinone and/or methylisothiazolinone in cosmetic products—A market survey
Authors: Sukakul Thanisorn , Kanchanapenkul Dollaporn , Bunyavaree Monthathip , Limphoka Pichaya , Kumpangsin Titinun , Boonchai Waranya 
Published: November 2018

BackgroundThere was a global epidemic of methylchloroisothiazolinone (MCI) and/or methylisothiazolinone (MI) contact allergy from 2009 to 2015. In response, the Thai Ministry of Public Health regulated the use of MCI/MI in cosmetics.ObjectiveTo survey the presence of MCI/MI and MI alone, as labelled on cosmetics sold on the Thai market, before and after the ministerial directive.MethodsThe presence of MCI and/or MI in leave‐on and rinse‐off cosmetics sold on the market, based on the labelling of ingredients in 3445 products, was analysed.ResultsBefore the implementation date, most leave‐on products contained MCI/MI. After the regulations came into force, the only leave‐on cosmetic subcategories that complied with the law were facial skin‐care, sunscreen and make‐up products. MCI/MI and MI alone were found on the labels of both leave‐on and rinse‐off products, the presence of each varying between product subcategories.ConclusionsDespite the ministerial regulations restricting their use, MCI and/or MI are still found in cosmetics sold on the Thai market. Dermatologists should be aware of this situation, and counsel patients to avoid products containing MCI and/or MI.
Does Cancellation of Preferential Tax Policy Reduce Foreign Direct Investment Inflows?
Authors: Luo Zhi , Wang Chen , Zhang Xun 
Published: November 2018

AbstractIn light of recent tax cuts by the US, should China reintroduce a preferential tax policy to attract foreign direct investment? This paper investigates whether China's 2008 tax policy change affected inward foreign direct investment. In contrast to previous studies, we break foreign investment down into suspect and real foreign investment using firm‐level data from 1998 to 2008 and conduct a difference‐in‐difference estimation to determine the effect of the tax policy change on both types of foreign investment and compare these to the effect on domestic investment. The results show that the 2008 tax policy change reduced the amount of suspect foreign investment and its effect on real foreign investment was insignificant, indicating that foreign firms in China are more concerned with the investment environment and economic stability than taxes. Therefore, China should create a regulated business environment instead of readopting supernational treatment for foreign enterprises.
Basic Considerations for the Use of Monoclonal Antibodies in Migraine
Authors: Levin Morris , Silberstein Stephen D. , Gilbert Robert , Lucas Sylvia , Munsie Leanne , Garrelts Alyssa , Kennedy Kate , Everman Nicole , Pearlman Eric 
Published: November 2018

BackgroundMigraine impacts more than 36 million people in the United States and 1 billion people worldwide. Despite the increasing availability of acute and preventive therapies, there is still tremendous unmet need. Potential treatments in development include monoclonal antibodies (mAbs). Appropriate use of these “biologic” treatments will necessitate an understanding of the aspects that distinguish them from traditional medications.AimMany drug classes are prescribed for migraine treatment, but all have limitations. Recently, calcitonin gene‐related peptide (CGRP) activity has shown a significant promise as a target for preventive therapy. In this review, we provide an overview of the potential role of CGRP mAbs in migraine, with a focus on their design, pharmacokinetics, safety, and immunogenicity.ConclusionsThe CGRP mAbs are an innovative new therapy for migraine and address the need for effective and tolerable preventive options. MAbs, including those that target CGRP or its receptor, bind to a target with high specificity and affinity and lead to few off‐target adverse effects, although mechanism‐based adverse reactions may occur. Unlike other therapeutic antibodies used to treat neurologic disease, CGRP mAbs do not have a target within the immune system and have been designed to avoid altering the immune system. The safety and efficacy of mAbs against CGRP or its receptors are being investigated in clinical development programs, and the first of these therapies has received regulatory approval in the United States.
Circulating tumor cells detected using fluid‐assisted separation technique in esophageal squamous cell carcinoma
Authors: Choi Mun Ki , Kim Gwang Ha , I Hoseok , Park Su Jin , Lee Moon Won , Lee Bong Eun , Park Do Youn , Cho Yoon‐Kyoung 
Published: November 2018

AbstractBackground and AimEsophageal squamous cell carcinoma (ESCC) is one of the aggressive gastrointestinal tract cancers. Detection of circulating tumor cells (CTCs) in peripheral blood from patients with various malignancies has been reported to have diagnostic, prognostic, and therapeutic implications. We aimed to evaluate CTCs in patients with ESCC and assess the clinical significance of CTCs in the early diagnosis of ESCC.MethodsPeripheral blood samples for CTCs analyses were prospectively obtained from 73 patients with ESCC prior to treatment between March 2015 and June 2018. CTCs were detected using a centrifugal microfluidic system with a new fluid‐assisted separation technique. Blood samples from 31 healthy volunteers were used as controls.ResultsAfter creating a receiver operating characteristic curve to determine the optimal CTC threshold to differentiate patients with ESCC from healthy controls, sensitivity and specificity were most optimized at a CTC threshold of two per 7.5 mL of blood. Among 66 subjects with ≥ 2 CTCs per 7.5 mL of blood, 63 (95.5%) had ESCC. Among 38 subjects with < 2 CTCs per 7.5 mL of blood, 28 (73.7%) were healthy controls. When using this threshold, the sensitivity and specificity for differentiating patients with ESCC from healthy controls were 86.3% and 90.3%, respectively. CTC count was associated with tumor–node–metastasis stage, especially lymph node metastasis, but there was no correlation with any other relevant clinicopathologic variable.ConclusionsOur results suggest that CTCs detected using fluid‐assisted separation technique could be helpful for early diagnosis of ESCC. Further large‐scale prospective studies are warranted to validate our findings.
Estimated Pulmonary Artery Systolic Pressure and Mortality in Older‐Elderly Heart Failure Patients
Authors: Matsushita Kenichi , Sakata Konomi , Satoh Toru , Yoshino Hideaki 
Published: November 2018

OBJECTIVESTo evaluate the association between high estimated pulmonary artery systolic pressure (ePASP) obtained by echocardiography and 1‐year mortality in patients with acute heart failure (HF), comparing findings in individuals aged 80 and older with those of individuals younger than 80.DESIGNRetrospective cohort study.SETTINGKyorin University Hospital.PARTICIPANTSIndividuals with acute decompensated HF (N = 335).MEASUREMENTSHigh ePASP was defined as a tricuspid regurgitation pressure gradient greater than 47 mmHg (ePASP >50 mmHg). Potential risk factors for 1‐year mortality were selected using univariate analysis followed by multivariate Cox regression analysis with backward stepwise selection of variables with P < .10 on univariate analysis to identify significant factors.RESULTSIn individuals aged 80 and older, high ePASP (hazard ratio (HR)=3.07; 95% confidence interval (CI)=1.21–7.80), discharge medications without diuretics (HR=4.18, 95% CI=1.66–10.54), and discharge medications without renin–angiotensin–aldosterone system inhibitors (HR=3.38, 95% CI=1.29–8.81) were independent risk factors for 1‐year mortality. In contrast, low systolic blood pressure at admission was the sole independent risk factor for 1‐year mortality (HR=0.94, 95% CI=0.89–0.99) in those younger than 80.CONCLUSIONHigh ePASP is a significant predictor of 1‐year mortality in individuals aged 80 and older with acute HF but not in those younger than 80. Elucidation of the pathophysiological mechanisms behind these findings should facilitate the development of more effective individualized therapies for older adults with acute HF. J Am Geriatr Soc 67:323–328, 2019.