bluuebunny/crossref_metadata_2025 huggingface dataset:
The dynamics of mangrove forest: the relationship between mangrove community structures and carbon stock–study cased in the Jakarta Bay
Authors: Sari N , Patria M P , Soesilo T E B , Tejakusuma I G
Published: August 2019

Pollution has resulted degradation that affects carbon stocks and mangrove composition and structure. Ecologically this relationship creates conditions that are interrelated with each other. This research has been conducted along in the shores of Jakarta Bay, from Tangerang (Banten Province)-North Jakarta (DKI Jakarta)- Muara Bendera (Bekasi-West Java province). The purpose of this research is to design the relationship between mangrove community structure and carbon stock. The method used vegetation analysis, allometric, Pearson correlation, and system dynamic. The result is the average of import value index at tree level is 113.57%, at tillers level is 92.03%, and the seedling levels is 80.6%. The average coverage for all levels was 38.62%, and according to regulation ministry of environment and forestry (MoEF) number 201 in years 2004, it was put into damaged criteria. Dominant species are performed by Avicennia marina, Avicennia lanata, Rhizophora aviculata, Soneratia caseolaris, and Soneratia alba. The average of carbon stock was 204.25 grC.m-2 with an average of 454.04 grC.m-2 biomass, an average litter of 271.59 grC.m-2, an average sediment of 206.31 grC.m-2, an average of roots of 45.4 grC.m-2, and average of nekromassa of 43.88 grC.m-2. Carbon stocks in above of soil surface was 67% of the total, and in below ground level was 33% of the total. The result of Pearson correlation showed a negative relationship between mangrove community structure and carbon stocks. This linear relationship shows the interplay between them. The low value of the mangrove community structure causes a low value in carbon stocks, and they were trying to balance in ecosystem. This is strengthening the hypothetic that the degradation occupied the mangrove forest and occurred for a long time. By looking at the ecological design which is explains their relationship, it is predicted that the Jakarta Bay will lose mangrove forest in the next around 40’s years, if the habitat condition remains the same as it is today.
Sustainable and self-sufficient farming practices: a social perspective on action research implementation in agriculture development (a case study in Pamalayan, Garut, Indonesia)
Authors: Nugraha A , Supyandi D , Heryanto M A
Published: August 2019

The introduction of new technology and innovation in agriculture development processes often unable to cope with the dynamics of field condition, which resulted in failures. This was due to the inability of development model to include the dynamic complexities of the field situation. Action research was then emerged as one of the solutions in order to reduce the gap between the ‘lab’ and ‘real world’. This study was aimed to evaluate the dissemination process of sustainable and self-sufficient farming practices that was carried by Indonesian Institute of Science through Action Research Approach in Pamalayan Village, Garut, Indonesia. This paper stresses on the social part of the dissemination process to grasp understanding of how the dynamics of knowledge transfer took place in the process. The study was a case study, applying descriptive qualitative method through the application of outcome mapping approach. Data were collected through in-depth interviews with key actors (farmers, institutions, researchers), participant observation, and document analysis. The results showed that the characteristics of leader as vanguard and gate keeper was the main key of success of this program. Aside of that, the informal style of dissemination by living and doing things together was proved to be very effective in reassuring the process of development. Through those approaches, development actors could build trust, sense of belonging, and even enhance the social cohesions in situ. This study could provide better understanding for the policy/program designer, so that they will, in the future, take social dynamics into account. Furthermore, this study can also provide some bases for scaling up similar ideas in different areas.
Sustainable local rice development (a case of pandanwangi rice development in Cianjur, Indonesia)
Authors: Supyandi D , Sukayat Y , Charina A
Published: August 2019

The development of local rice in Indonesia must always be encouraged, in addition to a way to maintain the wealth of germplasm, also because its uniqueness is the source of its advantage. Although a lot of local rice varieties have not been developed, a number of unique rice varieties have their own market share and make them premium rice varieties, such as pandanwangi. In Indonesia, pandanwangi rice has been known as a superior rice having a distinctive taste and aroma, and has high economic value. Technically, pandanwangi rice cultivation is different from other rice varieties that are massively developed in Indonesia such as IR or Ciherang. Due to its characteristics, pandanwangi rice cultivation requires a higher effort and longer cultivation time than the others. This paper briefly describes the objective conditions of pandanwangi rice, particularly related to the problems in its development, describes the social relation among institutions to develop pandanwangi varieties, and describes strategic changes needed to improve pandanwangi rice performance. This paper is a mix of field visit results, through in-depth interview and FGD, and literature review relating to issues above. The result shows that in pandanwangi case, high potential has not automatically resulted in high development of the variety as well as farmer wealth. Several problems from on farm conditions to regulatory policies have brought about low growth or even stagnant development of pandanwangi. Economic aspects were not the main motivation of farmers to cultivate, compared to social aspects and the power of regulator. Hence, in order to improve pandanwangi performance to be competitive, integration among actors, institutions and learning processes is definitely necessary.
Heading towards sustainable cacao agribusiness system (a case study in North Luwu, South Sulawesi, Indonesia)
Authors: Nugraha A , Heryanto M A , Wulandari E , Pardian P
Published: August 2019

Cacao is one of the most potential estate crops in Indonesia, which are traded worldwide. At one hand, many efforts were conducted to improve its performance in terms of production, productivity, value added, and competitiveness. On the other hand, those efforts somehow pose threats to long term sustainability, environmentally and socio-economically. This study was aimed to reveal the complexity of the pathway towards sustainable cacao development in North Luwu, South Sulawesi, by providing a generic map of causal effect between elements that has role in North Luwu’s cacao agribusiness system. The study was a qualitative study, relying on the depth of information gained through in-depth interviews with key actors, observations and document analysis. Information were then analyzed by using system thinking approach, which then illustrated in a causal loop diagram to show the dynamics in the system. The result shows that in practice, cacao agribusiness system is very complex due to the interrelatedness of technical aspects, social aspects, environmental aspects and economic aspects. The synchronization of all those aspects are very important in order to reach sustainability in cacao agribusiness system.
Readiness of youth in rural agribusiness (case of West Java, Indonesia)
Authors: Setiawan I , Sumardjo  , Satria A , Tjitropranoto P
Published: August 2019

As a system, agribusiness is complex in its nature. The consequence is, whoever wants to enter the system is required to be ready. The complexity of agribusiness has made it less liked and under-valued by the youth. The implication of this is that the age structure of agribusiness agents in Indonesia became older. Paradox to that, it is identified that in West Java plateau, educated and skilled youths choose to enter into agribusiness. This research aimed to: (1) descriptively analyse the readiness of agribusiness young actors (AYA) in performing agribusiness; (2) analyse the readiness difference of AYA; (3) analyse personal, interesting and push factors that influence the readiness of AYA, and; (4) formulate readiness reinforcement strategy for AYA. This research designed integrally and conducted in West Java for 10 months (July 2014 - July 2015). Primary data was collected from structured interview with 280 respondents, then was tabulated and analysed statistically using SEM and LISREL 8.80 analysis tools. The result of the research shows that the readiness of AYA is high. The readiness of AYA is evidently different across areas. This readiness is manifestly influenced by pull factors as well as personal characteristic. In order to gain readiness earlier, those interesting factors as well as dominant personal character should become the primary contents in young agents’ extension. The recommendation is to develop a synergy with stakeholders through multiple helix extension.
Effect of annealing on specific magnetization of Fe-Cr-Nb-Cu-Si-B with the partial replacement of Fe by chromium
Authors: Iqbal M Zashed , Hossain M A , Gafur M A , Mahmud Md Sultan , Saha D K , Sikder S S
Published: August 2019

The samples Fe73.5-xCrxNb3Cu1Si13.5B9 [x = 7, 9, 10 and 12.5 are prepared in the amorphous state in the form of thin ribbons by rapid quenching technique at wheel speed of 25 m s−1 in an Ar atmosphere. The composition was sintered at the temperature 450–8000 C for half an hour. The saturation magnetization (Ms) and Curie temperature (Tc) of these alloys decrease linearly with the increase of Cr content for the entire composition range due to dilution of Fe magnetic moment and weakening of exchange interaction between of magnetic atoms. The critical composition for disappearance of ferromagnetism fall of curve Ms with the replacement Fe by Cr, where the nearest neighbor coupling is longer dominant and intermediate range occur, giving rise to a significant portion of antiferromagnetic interaction. The Curie temperature decreases due the weaker interaction among the Fe magnetic moment. The structural relaxation is associated with the magnetization up to the annealed temperature 600 °C and the chemical disorderness arise with reference to enhancement of M of annealed samples. M versus H curves sharply rise which indicates the formation of crystallization and it seems to ferromagnetic and for x = 12.5 which is paramagnetic in the amorphous condition with Tc = 246 K. This increase of M for the four samples are due to the evolution of ferromagnetic α-Fe (Si) nanograin crystal.
Incentivizing New Veterinary Pharmaceutical Products to Combat Antibiotic Resistance
Authors: Sneeringer Stacy , Clancy Matt
Published: August 2019

The development of alternative animal health products is one way to reduce antibiotic use in agriculture. However, little economic research is directed at animal pharma. While programs to incentivize research and development (R&D) for human drugs have been adopted, analogous programs in veterinary pharma are only at the proposal stage. We describe the broad “push” and “pull” incentive mechanisms for human pharma, and analyze the differences in employing these in veterinary pharma. Using newly compiled data on veterinary drug approvals and firm‐level R&D, we also present data on trends in drug development for veterinary pharma.
Invasive Japanese Barberry, Berberis thunbergii (Ranunculales: Berberidaceae) Is Associated With Simplified Branch-Dwelling and Leaf-Litter Arthropod Communities in a New York Forest
Authors: Clark Robert E , Seewagen Chad L
Published: August 2019

Arthropod food webs can be indirectly impacted by woody plant invasions, with cascading consequences for higher trophic levels. There are multiple bottom-up pathways by which invasive plants can alter food webs: above-ground interactions based on plant-herbivore associations and below-ground at the interface of leaf-litter and soil food webs. We compared arthropod community composition in these two food web dimensions in a New York forest that has been heavily invaded by nonnative Japanese barberry. Using two sampling protocols, we compared arthropod community composition on Japanese barberry shrubs to multiple species of native host shrubs and then compared leaf-litter arthropod assemblages between forest patches with exceptionally high Japanese barberry densities and those with relatively little to no Japanese barberry present. Fitting with trends in other woody shrub invasions, arthropod species richness was significantly lower in the leaf litter around Japanese barberry and on Japanese barberry plants themselves. Although overall arthropod abundance was also significantly lower on and in the leaf litter around Japanese barberry than on and around native shrubs, total biomass did not differ due to the taxa associated with Japanese barberry tending to be larger-bodied. We observed a dramatic reduction in predatory arthropods in response to both bottom-up pathways, particularly among ants and spiders. Our results show that Japanese barberry-invaded habitats may be experiencing trophic downgrading as result of lower numbers of generalist predators like spiders and ants, which may have rippling effects up the food web to insectivorous animals and their predators.
The association between obesity and cardiovascular disease mortality in different strata of socioeconomic position: evidence from pooled Norwegian health surveys
Authors: Kjøllesdal Marte , Degerud Eirik , Næss Øyvind
Published: August 2019

Background

Socioeconomic position (SEP) is related to both obesity and cardiovascular disease (CVD). There is little evidence on whether SEP modifies the relation between obesity and CVD. The aim of the study was to investigate whether the association between obesity and CVD mortality is stronger among people with disadvantaged than among people with advantaged life course SEP.

Methods

Data from Norwegian population-based cardiovascular health surveys (1985–2003), including body mass index and CVD risk factors (cholesterol, blood pressure, smoking, current treatment for hypertension) were linked to socioeconomic indicators from register and census data (1960–90), and to the Cause of Death Registry (up until 2014). The total number of participants was 398 297.

Results

In comparison with normal weight, the age-adjusted hazard ratios and 95% confidence intervals of CVD mortality among obese participants were 2.39 (2.07–2.75) and 2.08 (1.70–2.53) among men and women with high SEP, respectively and 1.88 (1.60–2.21) and 1.75 (1.43–2.14) among men and women with low SEP. Adjustment for CVD risk factors attenuated the results in a similar manner in all SEP groups, and among both women and men.

Conclusion

Obesity was consistently associated with a higher risk of CVD mortality, with only minor variation according to SEP. This means that preventing or treating obesity is, for the purpose of reducing CVD risk, equally important for an individual with high or low SEP.
Global patterns of avian influenza A (H7): virus evolution and zoonotic threats
Authors: Naguib Mahmoud M , Verhagen Josanne H , Mostafa Ahmed , Wille Michelle , Li Ruiyun , Graaf Annika , Järhult Josef D , Ellström Patrik , Zohari Siamak , Lundkvist Åke , Olsen Björn
Published: August 2019

Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.
Lamin A/C dysregulation contributes to cardiac pathology in a mouse model of severe spinal muscular atrophy
Authors: Šoltić Darija , Shorrock Hannah K , Allardyce Hazel , Wilson Emma L , Holt Ian , Synowsky Silvia A , Shirran Sally L , Parson Simon H , Gillingwater Thomas H , Fuller Heidi R
Published: August 2019

Cardiac pathology is emerging as a prominent systemic feature of spinal muscular atrophy (SMA), but little is known about the underlying molecular pathways. Using quantitative proteomics analysis, we demonstrate widespread molecular defects in heart tissue from the Taiwanese mouse model of severe SMA. We identify increased levels of lamin A/C as a robust molecular phenotype in the heart of SMA mice and show that lamin A/C dysregulation is also apparent in SMA patient fibroblast cells and other tissues from SMA mice. Lamin A/C expression was regulated in vitro by knockdown of the E1 ubiquitination factor ubiquitin-like modifier activating enzyme 1, a key downstream mediator of SMN-dependent disease pathways, converging on β-catenin signaling. Increased levels of lamin A are known to increase the rigidity of nuclei, inevitably disrupting contractile activity in cardiomyocytes. The increased lamin A/C levels in the hearts of SMA mice therefore provide a likely mechanism explaining morphological and functional cardiac defects, leading to blood pooling. Therapeutic strategies directed at lamin A/C may therefore offer a new approach to target cardiac pathology in SMA.
The World Still Is Not Flat: Lessons Learned from Organismal Interactions with Environmental Heterogeneity in Terrestrial Environments
Authors: Sears Michael W , Riddell Eric A , Rusch Travis W , Angilletta Michael J
Published: August 2019

Over the past decade, ecologists and physiologists alike have acknowledged the importance of environmental heterogeneity. Meaningful predictions of the responses of organisms to climate will require an explicit understanding of how organismal behavior and physiology are affected by such heterogeneity. Furthermore, the responses of organisms themselves are quite heterogeneous: physiology and behavior vary over different time scales and across different life stages, and because physiological systems do not operate in isolation of one another, they need to be considered in a more integrated fashion. Here, we review case studies from our laboratories to highlight progress that has been made along these fronts and generalizations that might be made to other systems, particularly in the context of predicting responses to climate change.
Reference points for the length-based indicator Lmax5% for use in the assessment of data-limited stocks
Authors: Miethe Tanja , Reecht Yves , Dobby Helen
Published: August 2019

In the absence of abundance indices from scientific surveys or commercial sources, reliable length frequency data from sampled commercial catches can be used to provide an indirect assessment of fishing mortality. Length-based indicators are simple metrics which describe length frequency distributions. The length-based indicator Lmax5%, the mean length of the largest 5% of individuals in the catch, combined with appropriately selected reference points, can be used to evaluate the presence of very large individuals in the catch and hence determine exploitation level. Using analytical per-recruit models, we derive reference points consistent with a spawning potential ratio of 40%. The reference points depend on the life history parameters for natural mortality, maturity, and growth (M, Lmat, L∞, k, CVL∞). Using available simulation tools, we investigate the sensitivity of the reference points to errors in these parameters and explore the usefulness of particular reference points for management purposes for stocks with different life histories. The proposed reference points are robust to uncertainty in length at first capture, Lc, and take into account the maturation schedule of a species. For those stocks with high M/k ratios (>1), Lmax5%, combined with the appropriate reference point, can be used to provide a data-limited stock assessment.
The urgent case for expanded development assistance for health
Authors: Sachs Jeffrey D
Published: August 2019

The low-income developing countries require increased development assistance for health (DAH) to achieve Sustainable Development Goal 3, ‘Healthy Lives for All’. DAH has a proven track record. DAH expanded during 2001–2008, with significant health gains in the LIDCs, but then stopped expanding in the wake of the 2008 financial crisis. The Global Fund to Fight AIDS, TB and Malaria requires around US$31.8 billion during 2021–2023 to maintain a trajectory to end the three epidemics by 2030, yet donors have so far signaled that they are prepared to offer less than half that sum, around US$14 billion.
Effect of diabetes mellitus on TB drug concentrations in Tanzanian patients
Authors: Mtabho Charles M , Semvua Hadija H , van den Boogaard Jossy , Irongo Constantine F , Boeree Martin J , Colbers Angela , Burger David M , van Crevel Reinout , van der Ven Andre J A M , Kibiki Gibson S , Tostmann Alma , Aarnoutse Rob E
Published: August 2019

Background

Diabetes mellitus (DM) is associated with poor TB treatment outcome. Previous studies examining the effect of DM on TB drug concentrations yielded conflicting results. No studies have been conducted to date in an African population.

Objectives

To compare exposure to TB drugs in Tanzanian TB patients with and without DM.

Patients and methods

A prospective pharmacokinetic study was performed among 20 diabetic and 20 non-diabetic Tanzanian TB patients during the intensive phase of TB treatment. Plasma pharmacokinetic parameters of isoniazid, rifampicin, pyrazinamide and ethambutol were compared using an independent-sample t-test on log-transformed data. Multiple linear regression analysis was performed to assess the effects of DM, gender, age, weight, HIV status and acetylator status on exposure to TB drugs.

Results

A trend was shown for 25% lower total exposure (AUC0–24) to rifampicin among diabetics versus non-diabetics (29.9 versus 39.9 mg·h/L, P=0.052). The AUC0–24 and peak concentration (Cmax) of isoniazid were also lower in diabetic TB patients (5.4 versus 10.6 mg·h/L, P=0.015 and 1.6 versus 2.8 mg/L, P=0.013). Pyrazinamide AUC0–24 and Cmax values were non-significantly lower among diabetics (P=0.08 and 0.09). In multivariate analyses, DM remained an independent predictor of exposure to isoniazid and rifampicin, next to acetylator status for isoniazid.

Conclusions

There is a need for individualized dosing of isoniazid and rifampicin based on plasma concentration measurements (therapeutic drug monitoring) and for clinical trials on higher doses of these TB drugs in patients with TB and DM.
A tale of three subspecialties: Diagnosis recording patterns are internally consistent but Specialty-Dependent
Authors: Diaz-Garelli Jose-Franck , Strowd Roy , Ahmed Tamjeed , Wells Brian J , Merrill Rebecca , Laurini Javier , Pasche Boris , Topaloglu Umit
Published: August 2019

Background

Structured diagnosis (DX) are crucial for secondary use of electronic health record (EHR) data. However, they are often suboptimally recorded. Our previous work showed initial evidence of variable DX recording patterns in oncology charts even after biopsy records are available.

Objective

We verified this finding’s internal and external validity. We hypothesized that this recording pattern would be preserved in a larger cohort of patients for the same disease. We also hypothesized that this effect would vary across subspecialties.

Methods

We extracted DX data from EHRs of patients treated for brain, lung, and pancreatic neoplasms, identified through clinician-led chart reviews. We used statistical methods (i.e., binomial and mixed model regressions) to test our hypotheses.

Results

We found variable recording patterns in brain neoplasm DX (i.e., larger number of distinct DX—OR = 2.2, P < 0.0001, higher descriptive specificity scores—OR = 1.4, P < 0.0001—and much higher entropy after the BX—OR = 3.8 P = 0.004 and OR = 8.0, P < 0.0001), confirming our initial findings. We also found strikingly different patterns for lung and pancreas DX. Although both seemed to have much lower DX sequence entropy after the BX—OR = 0.198, P = 0.015 and OR = 0.099, P = 0.015, respectively compared to OR = 3.8 P = 0.004). We also found statistically significant differences between the brain dataset and both the lung (P < 0.0001) and pancreas (0.009<P < 0.08).

Conclusion

Our results suggest that disease-specific DX entry patterns exist and are established differently by clinical subspecialty. These differences should be accounted for during clinical data reuse and data quality assessments but also during EHR entry system design to maximize accurate, precise and consistent data entry likelihood.
Detecting reports of unsafe foods in consumer product reviews
Authors: Maharana Adyasha , Cai Kunlin , Hellerstein Joseph , Hswen Yulin , Munsell Michael , Staneva Valentina , Verma Miki , Vint Cynthia , Wijaya Derry , Nsoesie Elaine O
Published: August 2019

Objectives

Access to safe and nutritious food is essential for good health. However, food can become unsafe due to contamination with pathogens, chemicals or toxins, or mislabeling of allergens. Illness resulting from the consumption of unsafe foods is a global health problem. Here, we develop a machine learning approach for detecting reports of unsafe food products in consumer product reviews from Amazon.com.

Materials and Methods

We linked Amazon.com food product reviews to Food and Drug Administration (FDA) food recalls from 2012 to 2014 using text matching approaches in a PostGres relational database. We applied machine learning methods and over- and under-sampling methods to the linked data to automate the detection of reports of unsafe food products.

Results

Our data consisted of 1 297 156 product reviews from Amazon.com. Only 5149 (0.4%) were linked to recalled food products. Bidirectional Encoder Representation from Transformations performed best in identifying unsafe food reviews, achieving an F1 score, precision and recall of 0.74, 0.78, and 0.71, respectively. We also identified synonyms for terms associated with FDA recalls in more than 20 000 reviews, most of which were associated with nonrecalled products. This might suggest that many more products should have been recalled or investigated.

Discussion and Conclusion

Challenges to improving food safety include, urbanization which has led to a longer food chain, underreporting of illness and difficulty in linking contaminated food to illness. Our approach can improve food safety by enabling early identification of unsafe foods which can lead to timely recall thereby limiting the health and economic impact on the public.
The Pre-Trial Chamber’s Afghanistan Decision
Authors: Poltronieri Rossetti Luca
Published: August 2019

On 12 April 2019, Pre-Trial Chamber II (PTC II) of the International Criminal Court (ICC) issued a decision pursuant to Article 15(4) of the Rome Statute on the request of the Office of the Prosecutor (OTP) to open an investigation in the situation of Afghanistan, refusing for the first time to grant an authorization to investigate in a situation initiated proprio motu. The Chamber grounded its decision on a ‘prognostic’ analysis of the prospects for viable investigation and prosecution, leading to the conclusion that an investigation would not have been in the interests of justice. The present contribution examines the PTC’s approach in the Afghan situation, comparing it with previous practice in the context of authorization proceedings. It suggests that the Chamber’s approach to the definition of the scope of the investigation, as well as its interpretation and concrete application of the interests of justice clause, might represent an unreasonable encroachment on the OTP’s discretion. The article also examines the potential consequences of the Afghanistan decision in future cases and briefly touches upon the appellate proceedings instituted by the OTP and the legal representatives of victims. It finally argues that the current practice in authorization proceedings lacks reasonable consistency, and that a ‘third way’ between excessive deference and interventionism in the exercise of judicial supervision of discretionary choices needs to be developed in practice, in order to safeguard the credibility of the Court.
IDH1 fine-tunes cap-dependent translation initiation
Authors: Liu Lichao , Lu J Yuyang , Li Fajin , Xing Xudong , Li Tong , Yang Xuerui , Shen Xiaohua
Published: August 2019

The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.
Alien Invasion: The Case of the Western Conifer-Seed Bug (Heteroptera: Coreidae) in Chile, Overreaction, and Misidentifications
Authors: Faúndez Eduardo I , Carvajal Mariom A , Villablanca Javier
Published: August 2019

Leptoglossus occidentalis (Heidemann) is an invasive species introduced in Europe, Asia, and most recently South America. In the present study, we report the overreaction situation caused by this bug in Chile, as it has been confused with kissing bugs (Reduviidae: Triatominae), Chagas’ disease vectors. During 2018 and first months of 2019, we received 74 alleged cases of kissing bugs to confirm identification. From these, a total of 63 were identified as L. occidentalis, representing a 85% of the total denounces. Additionally, the first bite case in a human is described. The situation caused by L. occidentalis in Chile is discussed, and an illustrated table is provided to correctly identify this species and tell it apart from Triatomines. It is concluded that L. occidentalis is well established in Chile, and it is necessary to educate the population on recognition of the bug and to avoid overreaction as the species can inflict painful bites, but not transmit any disease.
Very late locally recurrent chromophobe renal cell carcinoma: 15 years following radical nephrectomy for low-stage disease
Authors: Ismail Asmaa , Elmansy Hazem , Shahrour Walid , Prowse Owen , Kotb Ahmed
Published: August 2019

The majority of patients with renal cell carcinoma develop recurrence within 5 years following radical nephrectomy. Very late sole local recurrence beyond 10 years is rare, and all reported cases had clear cell histology. Surgical resection of local recurrence remains the best option for disease management. This case opens the way for further studying the rare histological variants of renal cancer and to encourage prolonged follow-up and offering surgery as the best option for managing these cases.
The ABCD database: a repository for chemically defined antibodies
Authors: Lima Wanessa C , Gasteiger Elisabeth , Marcatili Paolo , Duek Paula , Bairoch Amos , Cosson Pierre
Published: August 2019

The ABCD (for AntiBodies Chemically Defined) database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases of chemical and protein entities. It is freely available to the academic community, accessible through the ExPASy server (https://web.expasy.org/abcd/). The ABCD database aims at helping to improve reproducibility in academic research by providing a unique, unambiguous identifier associated to each antibody sequence. It also allows to determine rapidly if a sequenced antibody is available for a given antigen.
Patient Satisfaction Ratings of Male and Female Residents Across Subspecialties
Authors: Udawatta Methma , Alkhalid Yasmine , Nguyen Thien , Ong Vera , Woodard Jos’lyn , Sheppard John P , Duong Courtney , Iyengar Sonia , Migdal Christopher W , Mosley Virgie , Yang Isaac
Published: August 2019

BACKGROUND

Females currently comprise approximately 50% of incoming medical students yet continue to be underrepresented in certain medical subspecialties.

OBJECTIVE

To assess whether gender plays a role in patients’ perception of physician competency among different specialties.

METHODS

We administered surveys at 2 academic medical centers to patients who were stable, cognitively aware, and indicated English as their primary language. Survey questions evaluated communication, medical expertise, and quality of care.

RESULTS

A total of 4222 surveys were collected. Females comprised around half (n = 2133, 50.7%) of evaluated residents. First-year (n = 1647, 39%) and second-year (n = 1416, 33.5%) residents were assessed most frequently. Internal medicine conducted the most surveys (n = 1111, 23.6%), whereas head and neck surgery conducted the least (n = 137, 3.24%). There was no statistically significant difference between patients’ perception of male and female residents of the same year in overall communication skills, medical expertise, and quality of medical care. Female residents outperformed their male counterparts on specific questions evaluating the communication of treatment plans, patient education, and patient satisfaction (P < .001, P = .03, P = .04, respectively). Unsurprisingly, patients’ perceptions of residents’ overall communication skills, medical expertise, and quality of medical care significantly improved when comparing more experienced residents to newer residents.

CONCLUSION

There is no difference between overall communication, medical expertise, and quality of care between sexes, and across subspecialties. Though gender inequalities currently exist most starkly in practitioners in surgical subspecialties, women in surgical residencies were much better communicators than their male counterparts, but still perceived to have similar levels of medical expertise and quality of care.
Assessing the Differences in Measurement of Degree of Spondylolisthesis Between Supine MRI and Erect X-Ray: An Institutional Analysis of 255 Cases
Authors: Alvi Mohammed Ali , Sebai Adeeb , Yolcu Yagiz , Wahood Waseem , Elder Benjamin D , Kaufmann Timothy , Bydon Mohamad
Published: August 2019

BACKGROUND

Degenerative spondylolisthesis is the displacement of one vertebral body over the adjacent one. While standing and flexion-extension X-rays are preferred for determining listhesis, magnetic resonance imaging (MRI) is often utilized to assess the compression of nerve root or spinal cord.

OBJECTIVE

To investigate the difference in radiographic measurements of spondylolisthesis between X-rays and MRI.

METHODS

We retrospectively reviewed the records and radiographic images of patients with a confirmed diagnosis of spondylolisthesis undergoing operation in 2016. Primary variable of interest was the degree of slippage as per the Meyerding method. Agreement between the 2 reviewers was assessed using the 2-way intraclass correlation coefficient (ICC) for slippage percentage and Cohen's Kappa for grade. Agreement of Meyerding grade between the 2 imaging techniques was assessed using Cohen's Kappa, while the slip percentage measured for each technique was compared using a Bland-Altman (BA) plot, mean difference (MD), and 1-way ICC.

RESULTS

A total of 255 cases were analyzed. ICC between the 2 reviewers was found to be 0.75 (95% confidence interval [CI] = 0.64-0.83, P < .001) for X-ray and 0.76 (95% CI = 0.66-0.83, P < .001) for MRI. Agreement between X-ray and MRI for grading of spondylolisthesis was found to be poor (kappa = 0.32, P < .001). BA plot between X-ray and MRI measurements revealed an MD of 4.4% (95% limits of agreement: –10.3% to 19.3%) with 5.16% observations outside the limits of agreement and 1-way ICC of 0.35 showing poor agreement.

Conclusion

Our results demonstrate the discrepancy of spondylolisthesis grade measurements between weight-bearing X-ray and nonweight-bearing MRI. Careful evaluation of both imaging technique is warranted to determine the final severity of pathology and tailoring of management plan.
DISSEQT—DIStribution-based modeling of SEQuence space Time dynamics†
Authors: Henningsson R , Moratorio G , Bordería A V , Vignuzzi M , Fontes M
Published: August 2019

Rapidly evolving microbes are a challenge to model because of the volatile, complex, and dynamic nature of their populations. We developed the DISSEQT pipeline (DIStribution-based SEQuence space Time dynamics) for analyzing, visualizing, and predicting the evolution of heterogeneous biological populations in multidimensional genetic space, suited for population-based modeling of deep sequencing and high-throughput data. The pipeline is openly available on GitHub (https://github.com/rasmushenningsson/DISSEQT.jl, accessed 23 June 2019) and Synapse (https://www.synapse.org/#!Synapse: syn11425758, accessed 23 June 2019), covering the entire workflow from read alignment to visualization of results. Our pipeline is centered around robust dimension and model reduction algorithms for analysis of genotypic data with additional capabilities for including phenotypic features to explore dynamic genotype–phenotype maps. We illustrate its utility and capacity with examples from evolving RNA virus populations, which present one of the highest degrees of genetic heterogeneity within a given population found in nature. Using our pipeline, we empirically reconstruct the evolutionary trajectories of evolving populations in sequence space and genotype–phenotype fitness landscapes. We show that while sequence space is vastly multidimensional, the relevant genetic space of evolving microbial populations is of intrinsically low dimension. In addition, evolutionary trajectories of these populations can be faithfully monitored to identify the key minority genotypes contributing most to evolution. Finally, we show that empirical fitness landscapes, when reconstructed to include minority variants, can predict phenotype from genotype with high accuracy.
Drug Legalization and Decriminalization Beliefs Among Substance-using and Nonusing Individuals
Authors: Hammond Alexis S. , Dunn Kelly E. , Strain Eric C.
Published: August 2019

Objectives:

There has been advocacy for legalization of abusable substances, but systematic data on societal beliefs regarding such legalization are limited. People who use substances may have unique beliefs about legalization, and this study assessed whether they would be in favor of drug legalization/decriminalization. It was hypothesized that those who use particular drugs (especially marijuana) would support its legalization/decriminalization, but that this would not be the case across all classes (especially opioids and stimulants).

Methods:

A nationwide sample of 506 adults were surveyed online to assess demographic characteristics, substance misuse, and beliefs regarding drug legalization/decriminalization. Legalization/decriminalization beliefs for specific drugs were assessed on an 11-point scale (0, strongly disagree; 10, strongly agree).

Results:

For persons with opioid misuse (15.4%), when asked about their agreement with: “heroin should be legalized,” the mean score was 4.6 (SEE = 0.4; neutral). For persons with stimulant misuse (12.1%), when asked about their agreement with: “cocaine should be legalized,” the score was 4.2 (0.5). However, for persons with marijuana misuse (34.0%), when asked about their agreement with: “medical marijuana should be legalized” the score was 8.2 (0.3; indicating agreement), and for “recreational marijuana” the score was also 8.2 (0.3).

Conclusions:

These results suggest that persons who used marijuana strongly support the legalization of both recreational and medical marijuana, whereas persons who primarily have opioid or stimulant misuse have less strongly held beliefs about legalization of substances within those respective categories. By including those who misuse drugs, these data assist in framing discussions of drug legalization and have the potential to inform drug policy considerations.
Recovery From Opioid Problems in the US Population: Prevalence, Pathways, and Psychological Well-Being
Authors: Hoffman Lauren A. , Vilsaint Corrie , Kelly John F.
Published: August 2019

Objectives:

Research has enhanced our understanding of opioid misuse prevalence and consequences, but few studies have examined recovery from opioid problems. Estimating national recovery prevalence and characterizing individuals who have resolved opioid problems can inform policy and clinical approaches to address opioid misuse.

Methods:

We conducted a cross-sectional investigation of a nationally-representative sample of US adults who reported opioid problem resolution (OPI). For reference, OPI was compared with an alcohol problem resolution group (ALC). Analyses estimated OPI/ALC prevalence, differences in treatment/recovery service use, and psychological well-being, within 2 recovery windows: <1 year (early recovery) and 1 to 5 years (mid-recovery) since OPI/ALC problem resolution.

Results:

Of those who reported alcohol or drug use problem resolution, weighted problem resolution prevalence was 5.3% for opioids (early recovery 1.2%, mid-recovery 2.2%) and 51.2% for alcohol (early recovery 7.0%, mid-recovery 11.5%). In mid-recovery, lifetime use of formal treatment, pharmacotherapy, recovery support services, mutual help, and current pharmacotherapy were more prevalent in OPI than ALC. Service utilization did not differ between early-recovery OPI and ALC. Common services used by OPI included inpatient treatment (37.8%) and state/local recovery organizations (24.4%) in mid-recovery; outpatient treatment (25.7%) and recovery community centers (27.2%) in early recovery; Narcotics Anonymous (40.2%–57.8%) and buprenorphine-naloxone (15.3%–26.7%) in both recovery cohorts. Regarding well-being, OPI reported higher self-esteem than ALC in early recovery, and lower self-esteem than ALC in mid-recovery.

Conclusions:

An estimated 1.2 million American adults report resolving an opioid problem. Given the service use outcomes and longer-term problem resolution of mid-recovery OPI, early-recovery OPI may require encouragement to utilize additional or more intensive services to achieve longer-term recovery. OPI beyond recovery-year 1 may need enhanced support to address deficient self-esteem and promote well-being.
Should I Plan to Open? Predicting the Need for Open Reduction in the Treatment of Developmental Dysplasia of the Hip
Authors: Talathi Nakul S. , Trionfo Arianna , Patel Neeraj M. , Upasani Vidyadhar V. , Matheney Travis , Mulpuri Kishore , Sankar Wudbhav N.
Published: August 2019

Background:

Closed reduction is generally attempted on children under 18 months of age who present as older infants or who fail nonoperative management for developmental dysplasia of the hip (DDH). However, many of these patients will not achieve concentric reduction by closed means and will ultimately require open reduction (OR). Limited evidence exists to predict which patients can be adequately closed reduced versus those who will need open treatment.

Methods:

Prospectively collected data from 4 select centers of an international multicenter study group sharing a common treatment approach were reviewed for all DDH infants under 18 months old that required operative management. Patients were categorized into 2 groups: those whose hips were successfully closed reduced or those who ultimately required OR. Factors were compared between the closed reduction and OR groups for 2 separate cohorts—those presenting early in life with ultrasound (US) data, and those presenting later with radiographic data.

Results:

A total of 154 patients (166 hips) were included in the analysis. Overall, 87.3% were female. In the early-presenting cohort, purposeful entry multivariate regression revealed that patients with Graf IV hips on US had 3.8 times higher odds of requiring an OR. For the later cohort, hips that were clinically irreducible (ie, negative Ortolani sign) had 3.3 times higher odds of requiring OR. Patients with International Hip Dysplasia Institute (IHDI) grade IV hips had 2.5 times higher odds of needing an OR versus those with grade III hips and 15.4 times higher odds than those with grade II hips. Children with an IHDI grade IV hip and a negative Ortolani sign had 4.4 times higher odds of needing OR.

Conclusion:

Children younger than 18 months with dislocated hips who require OR are more likely to have a high-grade radiographic dislocation (IHDI grade IV), negative preoperative Ortolani sign, and a Graf IV classification on initial US. This information may help surgeons budget the use of operating room time and better counsel parents about intraoperative expectations.

Level of Evidence:

Level III—Prognostic.