bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility of a Collaborative At-Sea Sampling Program (CASP) for the California Spiny Lobster Commercial Fishery: Catch Characteristics and Implications for Management
Authors: Yaeger Keith G. , Culver Carolynn S. , Schroeter Stephen C. , Page Henry M. 
Published: April 2017

Abstract
Fisheries management, including the development of fishery management plans (FMPs), requires the best available scientific information. To address this need, we piloted a collaborative at-sea sampling program (CASP) among California commercial lobster fishermen, scientists, and fishery managers to develop scientifically rigorous protocols and collect, analyze, and interpret essential fisheries information (EFI). Significant differences in catch characteristics among three regions (South, North Coast, and Northwest Islands) were documented. Legal CPUE was generally similar among regions, whereas sublegal CPUE was consistently highest in the South, followed by the North Coast and Northwest Islands. Evaluation of size structure revealed that legal lobsters were significantly smaller, just larger than legal size, in the South than in the other two regions, suggesting a higher exploitation rate there. Despite this, the South had significantly more prerecruits than the northern regions, a fact not considered in present fishery models. We also found a female bias in the legal sex ratios in the north regions and in the sublegal sex ratios in all regions that could affect model parameters for trap vulnerability and reproductive capacity. A discrepancy in the average weight of legal lobster for the Northwest Islands was identified which has implications for the spawning potential ratio, a reference point that elicits management action. The regional variations in catch characteristics suggest that the California lobster fishery would benefit from using more sophisticated models that incorporate area-based EFI to better inform the harvest control rules. This finding supports the recommendations of the lobster FMP scientific review panel and the interests of resource managers, with the CASP data illustrating the value of the additional EFI and a mechanism for obtaining it. The demonstrated utility of the CASP for both cross-checking and providing additional data supports its ongoing use to inform management of the lobster fishery and as a model for other fisheries.
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington’s epigenetic landscape
Authors: Guo Jing , Zheng Jie 
Published: April 2017

Abstract

Motivation
The interpretation of transcriptional dynamics in single-cell data, especially pseudotime estimation, could help understand the transition of gene expression profiles. The recovery of pseudotime increases the temporal resolution of single-cell transcriptional data, but is challenging due to the high variability in gene expression between individual cells. Here, we introduce HopLand, a pseudotime recovery method using continuous Hopfield network to map cells to a Waddington’s epigenetic landscape. It reveals from the single-cell data the combinatorial regulatory interactions among genes that control the dynamic progression through successive cell states.

Results
We applied HopLand to different types of single-cell transcriptomic data. It achieved high accuracies of pseudotime prediction compared with existing methods. Moreover, a kinetic model can be extracted from each dataset. Through the analysis of such a model, we identified key genes and regulatory interactions driving the transition of cell states. Therefore, our method has the potential to generate fundamental insights into cell fate regulation.

Availability and implementation
The MATLAB implementation of HopLand is available at https://github.com/NetLand-NTU/HopLand.
The case for reindustrialisation in developing countries: towards the connection between the macroeconomic regime and the industrial policy in Brazil
Authors: Nassif André , Bresser-Pereira Luiz Carlos , Feijo Carmem 
Published: April 2017

AbstractThe majority of economic literature tends to discuss economic development issues by analysing the industrial policy and other long-term development policies separate from short-term macroeconomic policy. However, development strategies require a close coordination of the macroeconomic regime with the industrial policy. In addition to Brazil, our analytical discussion and normative implications can be addressed to other developing countries also facing premature deindustrialisation. We propose an analytical discussion of the phenomena of industrialisation, deindustrialisation and reindustrialisation, including a discussion on the connection between the macroeconomic regime and industrial policy, both oriented to reindustrialisation and catching up. The main point is that both policy regimes must be closely coordinated with each other. Concerning the macroeconomic regime, we argue that consistent monetary, fiscal, wage and exchange rate policies are those which are able to not only keep price stabilisation, but also provide average real interest rates below the average real return rates on capital, a competitive real exchange rate and real wage rates increasing in accordance with labour productivity growth. As for industrial policy, theoretical and empirical evidence suggest strategies aimed at the diversification of production, processes and products, especially within the manufacturing sector and within tradable segments of the service sector.
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
Authors: Bray Mark-Anthony , Gustafsdottir Sigrun M , Rohban Mohammad H , Singh Shantanu , Ljosa Vebjorn , Sokolnicki Katherine L , Bittker Joshua A , Bodycombe Nicole E , Dančík Vlado , Hasaka Thomas P , Hon Cindy S , Kemp Melissa M , Li Kejie , Walpita Deepika , Wawer Mathias J , Golub Todd R , Schreiber Stuart L , Clemons Paul A , Shamji Alykhan F , Carpenter Anne E 
Published: April 2017

Abstract

Background
Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each perturbation, such as a small molecule from a diverse library. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications.

Findings
This microscopy dataset includes 919 265 five-channel fields of view, representing 30 616 tested compounds, available at “The Cell Image Library” (CIL) repository. It also includes data files containing morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., per-well) level; the image analysis workflows that generated the morphological features are also provided. Quality-control metrics are provided as metadata, indicating fields of view that are out-of-focus or containing highly fluorescent material or debris. Lastly, chemical annotations are supplied for the compound treatments applied.

Conclusions
Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, such as target identification. Integration with genetically perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.
The shortest periodic and flaring flux variability of a methanol maser emission at 6.7 GHz in G 014.23−00.50
Authors: Sugiyama Koichiro , Nagase Katsura , Yonekura Yoshinori , Momose Munetake , Yasui Yasutaka , Saito Yu , Motogi Kazuhito , Honma Mareki , Hachisuka Kazuya , Matsumoto Naoko , Uchiyama Mizuho , Fujisawa Kenta 
Published: April 2017

Abstract
We detected flaring flux variability that regularly occurred with a period of 23.9 d on a 6.7 GHz methanol maser emission at Vlsr = 25.30 km s−1 in G 014.23−00.50 through highly frequent monitoring using the Hitachi 32 m radio telescope. Analyzing data from 2013 January 5 to 2016 January 21, the periodic variability has persisted in at least 47 cycles, corresponding to ∼1100 d. The period of 23.9 d is the shortest one observed in masers around high-mass young stellar objects so far. The flaring component normally falls below the detection limit (3 σ) of ∼0.9 Jy. In the flaring periods, the component rises above the detection limit with a ratio of the peak flux density more than 180 in comparison with the quiescent phase, showing intermittent periodic variability. The timescale of the flux rise was typically two days or shorter, and both symmetric and asymmetric profiles of flux variability were observed through intraday monitoring. These characteristics might be explained by a change in the flux of seed photons in a colliding-wind binary (CWB) system, or a variation of the dust temperature by the extra heating source of a shock formed by a CWB system within a gap region in a circumbinary disk, in which the orbital semi-major axes of the binary are 0.26–0.34 au.
Up-regulation of Intracellular Calcium Handling Underlies the Recovery of Endotoxemic Cardiomyopathy in Mice
Authors: Morse Justin C. , Huang Joanne , Khona Natasha , Miller Edward J. , Siwik Deborah A. , Colucci Wilson S. , Hobai Ion A. 
Published: April 2017

Abstract

Background
In surviving patients, sepsis-induced cardiomyopathy is spontaneously reversible. In the absence of any experimental data, it is generally thought that cardiac recovery in sepsis simply follows the remission of systemic inflammation. Here the authors aimed to identify the myocardial mechanisms underlying cardiac recovery in endotoxemic mice.

Methods
Male C57BL/6 mice were challenged with lipopolysaccharide (7 μg/g, intraperitoneally) and followed for 12 days. The authors assessed survival, cardiac function by echocardiography, sarcomere shortening, and calcium transients (with fura-2-acetoxymethyl ester) in electrically paced cardiomyocytes (5 Hz, 37°C) and myocardial protein expression by immunoblotting.

Results
Left ventricular ejection fraction, cardiomyocyte sarcomere shortening, and calcium transients were depressed 12 h after lipopolysaccharide challenge, started to recover by 24 h (day 1), and were back to baseline at day 3. The recovery of calcium transients at day 3 was associated with the up-regulation of the sarcoplasmic reticulum calcium pump to 139 ± 19% (mean ± SD) of baseline and phospholamban down-regulation to 35 ± 20% of baseline. At day 6, calcium transients were increased to 123 ± 31% of baseline, associated with increased sarcoplasmic reticulum calcium load (to 126 ± 32% of baseline, as measured with caffeine) and inhibition of sodium/calcium exchange (to 48 ± 12% of baseline).

Conclusions
In mice surviving lipopolysaccharide challenge, the natural recovery of cardiac contractility was associated with the up-regulation of cardiomyocyte calcium handling above baseline levels, indicating the presence of an active myocardial recovery process, which included sarcoplasmic reticulum calcium pump activation, the down-regulation of phospholamban, and sodium/calcium exchange inhibition.
Electroencephalography Predicts Poor and Good Outcomes After Cardiac Arrest: A Two-Center Study*
Authors: Rossetti Andrea O. , Tovar Quiroga Diego F. , Juan Elsa , Novy Jan , White Roger D. , Ben-Hamouda Nawfel , Britton Jeffrey W. , Oddo Mauro , Rabinstein Alejandro A. 
Published: April 2017

Objective:The prognostic role of electroencephalography during and after targeted temperature management in postcardiac arrest patients, relatively to other predictors, is incompletely known. We assessed performances of electroencephalography during and after targeted temperature management toward good and poor outcomes, along with other recognized predictors.Design:Cohort study (April 2009 to March 2016).Setting:Two academic hospitals (Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Mayo Clinic, Rochester, MN).Patients:Consecutive comatose adults admitted after cardiac arrest, identified through prospective registries.Interventions:All patients were managed with targeted temperature management, receiving prespecified standardized clinical, neurophysiologic (particularly, electroencephalography during and after targeted temperature management), and biochemical evaluations.Measurements and Main Results:We assessed electroencephalography variables (reactivity, continuity, epileptiform features, and prespecified “benign” or “highly malignant” patterns based on the American Clinical Neurophysiology Society nomenclature) and other clinical, neurophysiologic (somatosensory-evoked potential), and biochemical prognosticators. Good outcome (Cerebral Performance Categories 1 and 2) and mortality predictions at 3 months were calculated. Among 357 patients, early electroencephalography reactivity and continuity and flexor or better motor reaction had greater than 70% positive predictive value for good outcome; reactivity (80.4%; 95% CI, 75.9–84.4%) and motor response (80.1%; 95% CI, 75.6–84.1%) had highest accuracy. Early benign electroencephalography heralded good outcome in 86.2% (95% CI, 79.8–91.1%). False positive rates for mortality were less than 5% for epileptiform or nonreactive early electroencephalography, nonreactive late electroencephalography, absent somatosensory-evoked potential, absent pupillary or corneal reflexes, presence of myoclonus, and neuron-specific enolase greater than 75 µg/L; accuracy was highest for early electroencephalography reactivity (86.6%; 95% CI, 82.6–90.0). Early highly malignant electroencephalography had an false positive rate of 1.5% with accuracy of 85.7% (95% CI, 81.7–89.2%).Conclusions:This study provides class III evidence that electroencephalography reactivity predicts both poor and good outcomes, and motor reaction good outcome after cardiac arrest. Electroencephalography reactivity seems to be the best discriminator between good and poor outcomes. Standardized electroencephalography interpretation seems to predict both conditions during and after targeted temperature management.
Pilot Feasibility Study of Therapeutic Hypothermia for Moderate to Severe Acute Respiratory Distress Syndrome*
Authors: Slack Donald F. , Corwin Douglas S. , Shah Nirav G. , Shanholtz Carl B. , Verceles Avelino C. , Netzer Giora , Jones Kevin M. , Brown Clayton H. , Terrin Michael L. , Hasday Jeffrey D. 
Published: April 2017

Objectives:
Prior studies suggest hypothermia may be beneficial in acute respiratory distress syndrome, but cooling causes shivering and increases metabolism. The objective of this study was to assess the feasibility of performing a randomized clinical trial of hypothermia in patients with acute respiratory distress syndrome receiving treatment with neuromuscular blockade because they cannot shiver.

Design:
Retrospective study and pilot, prospective, open-label, feasibility study.

Setting:
Medical ICU.

Patients:
Retrospective review of 58 patients with acute respiratory distress syndrome based on Berlin criteria and Pao
2/Fio
2 less than 150 who received neuromuscular blockade. Prospective hypothermia treatment in eight acute respiratory distress syndrome patients with Pao
2/Fio
2 less than 150 receiving neuromuscular blockade.

Intervention:
Cooling to 34–36°C for 48 hours.

Measurements and Main Results:
Core temperature, hemodynamics, serum glucose and electrolytes, and P/F were sequentially measured, and medians (interquartile ranges) presented, 28-day ventilator-free days, and hospital mortality were calculated in historical controls and eight cooled patients. Average patient core temperature was 36.7°C (36–37.3°C), and fever occurred during neuromuscular blockade in 30 of 58 retrospective patients. In the prospectively cooled patients, core temperature reached target range less than or equal to 4 hours of initiating cooling, remained less than 36°C for 92% of the 48 hours cooling period without adverse events, and was lower than the controls (34.35°C [34–34.8°C]; p < 0.0001). Compared with historical controls, the cooled patients tended to have lower hospital mortality (75% vs 53.4%; p = 0.26), more ventilator-free days (9 [0–21.5] vs 0 [0–12]; p = 0.16), and higher day 3 P/F (255 [160–270] vs 171 [120–214]; p = 0.024).

Conclusions:
Neuromuscular blockade alone does not cause hypothermia but allowed acute respiratory distress syndrome patients to be effectively cooled. Results support conducting a randomized clinical trial of hypothermia in acute respiratory distress syndrome and the feasibility of studying acute respiratory distress syndrome patients receiving neuromuscular blockade.
Zika virus and assisted reproduction
Authors: Cordeiro Christina N. , Bano Rashda , Washington Cross Chantel I. , Segars James H. 
Published: April 2017

Purpose of review
Due to the fact that the Zika virus can be sexually transmitted, there is a potential risk for disease transmission at several stages of assisted reproduction. Such a possibility poses a serious challenge to couples pursing fertility with reproductive technologies. Here, we discuss what is known regarding Zika virus infection with respect to sexual transmission and correlate this knowledge with recent recommendations in the realm of infertility treatment.

Recent findings
Zika virus can be transmitted from infected men and women through vaginal, oral or anal intercourse. Zika virus RNA has been detected in blood, semen, cervical mucus and vaginal fluid. Currently, the Centers for Disease Control recommends that infected men wait 6 months, and infected women 8 weeks, prior to attempting pregnancy. Reproductive tissue donors should wait 6 months before giving a specimen.

Summary
Further study of Zika virus transmission in different reproductive tissues and establishment of validated testing methods for viral disease transmissibility are urgently needed. Reproductive technologists need to establish screening, testing and laboratory protocols aimed to reduce the risk of Zika virus transmission during assisted reproduction.
Ulnar Head Reconstruction with Microvascular Second Metatarsal
Authors: Cavadas Pedro C. , Thione Alessandro 
Published: April 2017

Background:
The distal radioulnar joint along with the interosseous ligament of the forearm and the proximal radioulnar joint, form a functionally integrated system responsible for the pronation–supination of the hand. The distal ulna, the so-called ulnar head, is an integral part of this system. Apart from its well-known role in forearm rotation, the ulnar head is essential in transverse load transmission through the distal radioulnar joint upon resisted elbow flexion. Autologous reconstruction of ulnar head would theoretically be beneficial with respect to prostheses.

Methods:
Three cases of ulnar head reconstruction with microvascular second metatarsal are reported herein including trauma, oncological, and congenital ethiologies.

Results:
The clinical result was good without complaints of instability.

Conclusions:
The cases included in this series, although heterogeneous, indicate that this treatment may be feasible also in postoncological resections and in congenital cases.
Decompression Retinopathy After Goniotomy in a Child: A Case Report
Authors: Burstein Eitan S. , Netland Peter A. 
Published: April 2017

Purpose:
To report a case of ocular decompression retinopathy that developed in a child after undergoing goniotomy for uncontrolled pediatric uveitic glaucoma.

Patient and Methods:
We describe an 11-year-old Hispanic boy with a history of idiopathic uveitis and elevated intraocular pressure (IOP) in both eyes. He developed marked elevation of the IOP in the right eye (44 mm Hg) despite glaucoma medical therapy.

Results:
The patient’s right eye was treated with goniotomy, with reduction of vision to 20/70 and IOP to between 4 and 7 mm Hg during the first week postoperatively. The retina developed diffuse hemorrhages, both deep and superficial. Many of these hemorrhages had white centers. The findings were consistent with decompression retinopathy. The retinal hemorrhages began to improve 2 weeks and had cleared by 6 weeks after surgery. The IOP measurements ranged between 14 and 16 mm Hg from 2 to 6 weeks after goniotomy and the vision returned to preoperative baseline of 20/20-2 in the right eye. Six weeks after the initial surgery, the left eye was treated with goniotomy with no complications.

Conclusions:
Ocular decompression retinopathy, an uncommon complication of glaucoma surgery, can occur after goniotomy.
Resistance to Narrowband Ultraviolet B Therapy Over Varicose Veins in Two Cases of Generalized Vitiligo
Authors: Roth Gretchen M. , Holcomb Zachary E. , Brown Barbara , Fine Jo-David , Powers Jennifer G. 
Published: April 2017

ABSTRACT
Vitiligo is a difficult-to-control disease with a devastating impact in the lives of many patients. An association has been shown between the Koebner phenomenon and the occurrence of skin depigmentation in vitiligo. However, the medical literature contains very little information regarding the relationship between varicose veins, a common comorbidity for many patients, and vitiligo skin lesions. We present two cases of generalized vitiligo in which patients experienced delayed or absent repigmentation exclusively over varicose veins after narrowband ultraviolet B therapy, despite repigmentation over the rest of the body. In one case, repigmentation occurred after varicose vein treatment. These patients highlight potential and previously unexplored interactions between varicose veins and response to vitiligo phototherapy. The impact of varicose veins on vitiligo treatment may inform future research ideas into the pathogenesis of this skin disease. Furthermore, these cases suggest a possible mechanism of improving local treatment response in vitiligo by addressing underlying varicose veins.
Reticulated Violaceous Eruption
Authors: Vazirnia Aria , Jacob Sharon E. 
Published: April 2017

ABSTRACT
Teledermatology is a term to describe the provision of dermatologic medical services through telecommunication technology. In this modality, there is transfer of medical information electronically (including history and visual data) on a patient in one location to a provider who is in another location (Roman & Jacob, 2015). The construct of the TeleDermViewPoint column is such that cases are presented in a standardized teledermatology reader format reflective of an actual teledermatology report. This is a case of a reticulated violaceous eruption.