bluuebunny/crossref_metadata_2025 huggingface dataset:
A case of ileus surgery using the water pressure method against ileus caused by incarceration into the inverted bladder diverticulum
Authors: Morioka Hirotsugu , Aoki Jun , Fujino Kazuyoshi , Sugahara Yuki , Orihata Michihiro , Goto Michitoshi , Kobayashi Shigeru , Okazawa Yu
Published: January 2020

Background

Ileus is quite a common disease, but is associated with various causes. As far as we know, there have only been one case of ileus due to inverted bladder diverticulum, which is extremely rare.

Case presentation

The patient was a 53-year-old male. He made an emergency visit to our hospital with a chief complaint of left lower quadrant pain. He underwent right inguinal hernia surgery at 2 years of age with no history of laparotomy. An abdominal enhanced CT revealed inversion of the bladder left side wall where part of enlarged small intestine was found. Ascites were also found between the incarcerated small intestine and the bladder, leading to a diagnosis of strangulation ileus due to internal hernia and subsequent emergency surgery. A laparotomy revealed incarceration of the small intestine in the bladder left wall as a Richter type. The incarceration was rigid. We believed it would be difficult to pull out by extraction. Therefore, we inserted a Nelaton catheter between the incarcerated small intestine and the bladder and carried out the water pressure method to release the ileus. We did not perform an enterectomy since no manifest necrosis or perforation of the small intestine was found. The inverted bladder wall was a partial depression. We interpreted it to be a bladder diverticulum. We made a suture for occlusion with the bladder diverticulum inverted. Ileus arising from inverted bladder diverticulum is a very rare disease state. We hereinafter report on this case along with bibliographical considerations.

Conclusions

We experienced a case of small intestine ileus due to inverted bladder diverticulum, which is very rare. In terms of preservation of the bowel, we believed the water pressure method to release the ileus was useful.
Massive hiatal hernia involving prolapse of the entire stomach and pancreas resulting in pancreatitis and bile duct dilatation: a case report
Authors: Tomida Hidenori , Hayashi Masahiro , Hashimoto Shinichi
Published: January 2020

Background

Hiatal hernia is defined by the permanent or intermittent prolapse of any abdominal structure into the chest through the diaphragmatic esophageal hiatus. Prolapse of the stomach, intestine, transverse colon, and spleen is relatively common, but herniation of the pancreas is a rare condition. We describe a case of acute pancreatitis and bile duct dilatation secondary to a massive hiatal hernia of pancreatic body and tail.

Case presentation

An 86-year-old woman with hiatal hernia who complained of epigastric pain and vomiting was admitted to our hospital. Blood tests revealed a hyperamylasemia and abnormal liver function test. Computed tomography revealed prolapse of the massive hiatal hernia, containing the stomach and pancreatic body and tail, with peripancreatic fluid in the posterior mediastinal space as a sequel to pancreatitis. In addition, intrahepatic and extrahepatic bile ducts were seen to be dilated and deformed. After conservative treatment for pancreatitis, an elective operation was performed. There was a strong adhesion between the hernial sac and the right diaphragmatic crus. After the stomach and pancreas were pulled into the abdominal cavity, the hiatal orifice was closed by silk thread sutures (primary repair), and the mesh was fixed in front of the hernial orifice. Toupet fundoplication and intraoperative endoscopy were performed. The patient had an uneventful postoperative course post-procedure.

Conclusion

A rare massive hiatal hernia, involving the stomach and pancreatic body and tail, can cause acute pancreatitis with bile duct dilatation. The etiology can be flexure of the main pancreatic and extrahepatic bile ducts. Symptomatic herniation is best treated with surgery. Elective surgery is thought to be safer than emergent surgery in patients with serious complications.
A case of esophagojejunal varices rupture after proximal gastrectomy with double-tract reconstruction
Authors: Shinno Naoki , Kawabata Ryohei , Furukawa Haruna , Goda Seiichi , Sueda Toshinori , Matsumura Tae , Koga Chikato , Noura Shingo , Shimizu Junzo , Okada Atsuya , Hasegawa Junichi
Published: January 2020

Background

The varices after proximal or total gastrectomy are uncommon because the supplying vessels are all divided. Emergent upper gastrointestinal endoscopy is the cornerstone of first-line management for the diagnosis and treatment of esophageal varices. However, there is no widely accepted standard strategy for esophagojejunal varices. We report a patient with esophagojejunal varices rupture 3 months after proximal gastrectomy treated with percutaneous transhepatic obliteration.

Case presentation

A 50-year-old man who had undergone proximal gastrectomy with double-tract reconstruction for esophagogastric junctional cancer 3 months before was admitted to the hospital due to gastrointestinal perforation. We performed emergency surgery and abdominal symptoms and inflammatory response improved postoperative. However, on POD3, he had eruptive bleeding at the just anal side of esophagojejunal anastomosis. Endoscopic clipping was unsuccessful because the mucosa was fragile and easily lacerated. Contrast-enhanced CT scan revealed the dilatation of the jejunal vein flowing into the ascending jejunal limb. Therefore, he was diagnosed as esophagojejunal varices rupture and percutaneous transhepatic obliteration (PTO) was tried for hemostasis. The portal and superior mesenteric veins were catheterized with the percutaneous transhepatic approach. Contrast agent injection into the jejunal branch demonstrated retrograde flow to the azygos vein through esophagojejunal varices. The microcatheter was inserted into the variceal blood supply branch and 10 mL of 5% ethanolamine oleate with iopamidol was injected. After obliteration therapy, the superior mesenteric venogram showed complete occlusion of the variceal supply branch. The patient was discharged from the hospital without any complications after 14 days.

Conclusion

PTO can be effective for gastroesophageal varices rupture with a dilated jejunal vein of the ascending limb, few supplying vessels, and little ascites.
The performance of the World Rugby Head Injury Assessment Screening Tool: a diagnostic accuracy study
Authors: Fuller G. W. , Tucker R. , Starling L. , Falvey E. , Douglas M. , Raftery M.
Published: January 2020

Background

Off-field screening tools, such as the Sports Concussion Assessment Tool (SCAT), have been recommended to identify possible concussion following a head impact where the consequences are unclear. However, real-life performance, and diagnostic accuracy of constituent sub-tests, have not been well characterized.

Methods

A retrospective cohort study was performed in elite Rugby Union competitions between September 2015 and June 2018. The study population comprised consecutive players identified with a head impact event undergoing off-field assessments with the World Rugby Head Injury Assessment (HIA01) screening tool, an abridged version of the SCAT3. Off-field screening performance was investigated by evaluating real-life removal-from-play outcomes and determining the theoretical diagnostic accuracy of the HIA01 tool, and individual sub-tests, if player-specific baseline or normative sub-test thresholds were strictly applied. The reference standard was clinically diagnosed concussion determined by serial medical assessments.

Results

One thousand one hundred eighteen head impacts events requiring off-field assessments were identified, resulting in 448 concussions. Real-life removal-from-play decisions demonstrated a sensitivity of 76.8% (95% CI 72.6–80.6) and a specificity of 86.6% (95% CI 83.7–89.1) for concussion (AUROC 0.82, 95% CI 0.79–0.84). Theoretical HIA01 tool performance worsened if pre-season baseline values (sensitivity 89.6%, specificity 33.9%, AUROC 0.62,p < 0.01) or normative thresholds (sensitivity 80.4%, specificity 69.0%, AUROC 0.75,p < 0.01) were strictly applied. Symptoms and clinical signs were the HIA01 screening tool sub-tests most predictive for concussion; with immediate memory and tandem gait providing little additional diagnostic value.

Conclusions

These findings support expert recommendations that clinical judgement should be used in the assessment of athletes following head impact events. Substitution of the tandem gait and 5-word immediate memory sub-tests with alternative modes could potentially improve screening tool performance.
Feasibility of alcohol screening and brief intervention in primary health care in Kazakhstan: study protocol of a pilot cluster randomised trial
Authors: Schulte Bernd , O’Donnell Amy , Lahusen Harald , Lindemann Christina , Prilutskaya Mariya , Yussopov Oleg , Kaliyeva Zhanar , Martens Marcus-Sebastian , Verthein Uwe
Published: January 2020

Background

Identifying and addressing heavy drinking represents a major public health priority worldwide. Whilst the majority of alcohol screening and brief intervention (ASBI) research has been conducted in western, high-income countries, evidence is growing that ASBI can also impact positively on heavy drinkers in low- and middle-income country populations. This mixed methods study aims to assess the feasibility of conducting a fully randomised controlled trial of the effectiveness of ASBI in primary care in Kazakhstan and explore the feasibility and acceptability of implementing ASBI in this setting from patients’ and physicians’ perspectives.

Methods

Six primary health care units in the region of Pavlodar will be cluster randomised to either an intervention (WHO manualised 5 min alcohol brief intervention plus alcohol leaflet) or control group (simple feedback plus alcohol leaflet). Primary feasibility measures will be rates of participation at baseline and retention of eligible patients at the 3-month follow-up point. Patient/physician questionnaires and physician focus groups will assess additional dimensions of feasibility, as well as acceptability, according to the RE-AIM framework: Reach (rates of eligible patients screened/received advice); Effectiveness (change in AUDIT-C score); Adoption (rate/representativeness of participating physicians); Implementation (quality of ASBI/barriers and facilitators to delivery); and Maintenance (potential sustainability of intervention).

Discussion

This is the first trial of the feasibility and acceptability of ASBI in Kazakhstan. As the planning and assessment of implementation determinants is based on the RE-AIM framework, the project outcomes will be relevant for the future development, tailoring and implementation of ASBI in Kazakhstan.

Trial registration

DRKS, DRKS00015882, Registered 17 December 2018.
Factors influencing the persistence of reindeer lichens (Cladonia subgenus Cladina) within frequent-fire environments of the Mid-Atlantic Coastal Plain, USA
Authors: Ray David G. , Cahalan Gabriel D. , Lendemer James C.
Published: January 2020

Background

Prescribed fire is increasingly used to accomplish management goals in fire-adapted systems, yet our understanding of effects on non-target organisms remains underdeveloped. Terricolous lichens in the genus Cladonia P. Browne, particularly cushion-forming reindeer lichens belonging to Cladonia subgenus Cladina Nyl., fit into this category, being characteristic of fire-adapted ecosystems, yet highly vulnerable to damage or consumption during burns. Moreover, inherently slow dispersal and growth rates raise questions about how to conserve these taxa in the context of fire-mediated restoration management. This research was undertaken to identify factors that contribute to Cladonia persistence within areas subject to repeated burning and involved tracking the fate of 228 spatially isolated individuals distributed across seven sites previously burned zero to two times. Site selection was determined by edaphic factors associated with a rare inland dune woodland community type known to support relatively high densities of Cladonia.

Results

Evaluated across all sites, the post-burn condition of Cladonia subtenuis (Abbayes) Mattick samples, categorized as intact (32%), fragmented (33%), or consumed (36%) individuals, approximated a uniform distribution. However, their status was highly variable at the different sites, where from 0 to 70% were assessed as intact and 11 to 60% consumed. Machine-learning statistical techniques were used to identify the factors most strongly associated with fire damage, drawing from variables describing the proximate fuel bed, growth substrate, and fire weather. The final descriptive model was dominated by variables characterizing the understory fuel matrix.

Conclusions

Areas with highly contiguous fuels dominated by pyrogenic pine needles were most likely to result in consumption of individual Cladonia, whereas those growing in areas with low fuel continuity or in areas dominated by hardwood litter were more likely to persist (intact or as fragments). Further, substrates including bare soil and moss mats afforded more protection than coarse woody debris or leaf litter in settings where fuels were both contiguous and highly flammable. Our findings describe the characteristics of within-site fire refugia, the abundance of which may be enhanced over time through restoration and maintenance treatments including thinning, promotion of mixed-species overstory composition, and periodic burning. Because lichens contribute to, and are considered reliable indicators of forest health, fire-based restoration management efforts will benefit from improved understanding of how these vulnerable organisms are able to persist.
Integrated electrochemical processes for textile industry wastewater treatment: system performances and sludge settling characteristics
Authors: Afanga Hanane , Zazou Hicham , Titchou Fatima Ezzahra , Rakhila Youness , Akbour Rachid Ait , Elmchaouri Abdellah , Ghanbaja Jaafar , Hamdani Mohamed
Published: January 2020

Textile wastewater containing toxic dyes needs efficient treatment before being released into the environment. Certain dyes are known or presumed to have carcinogenic potential for humans. In this work, hybrid electrochemical processes including electrocoagulation (EC) alone and combined with electro Fenton (EF), anodic oxidation (AO) and peroxi-coagulation (PC) were tested to treat real textile wastewater using a batch reactor. A sequential EC and EF (EC-EF) process was found to be more effective. The experimental results indicated that the effectiveness of the treatment decreases in the following order: EC-EF > EC-AO > EC-PC > EC. EC-EF results showed a decrease in chemical oxygen demand (COD, 97%), total organic carbon (98%), total suspended solids (98%), and the concentration of metal species; showing that the treatment of such wastewater type can be achieved by combined EC-EF process in a one-pot bench-scale reactor. The electrical energy consumption, the iron dissolution, and the biological oxygen demand/COD ratios of EC and EC-EF processes were evaluated. Characterization of the sludge generated during EC treatment at current density of 20 mA cm− 2 was carried out. Precipitation, adsorption, and electrochemical oxidation/reduction of organic dyes and metallic ions occurred during the treatment. This investigation shows the efficiency of combined EC-EF to treat textile wastewater.
A Polygenic Risk Score Suggests Shared Genetic Architecture of Voice Break With Early Markers of Pubertal Onset in Boys
Authors: Lardone María C , Busch Alexander S , Santos José L , Miranda Patricio , Eyheramendy Susana , Pereira Ana , Juul Anders , Almstrup Kristian , Mericq Verónica
Published: January 2020

Context

Voice break, as a landmark of advanced male puberty in genome-wide association studies (GWAS), has revealed that pubertal timing is a highly polygenic trait. Although voice break is easily recorded in large cohorts, it holds quite low precision as a marker of puberty. In contrast, gonadarche and pubarche are early and clinically well-defined measures of puberty onset.

Objective

To determine whether a polygenic risk score (PRS) of alleles that confer risk for voice break associates with age at gonadarche (AAG) and age at pubarche (AAP) in Chilean boys.

Experimental Design

Longitudinal study.

Subjects and Methods

401 boys from the Growth and Obesity Chilean Cohort Study (n = 1194; 49.2% boys).

Main Outcome Measures

Biannual clinical pubertal staging including orchidometry. AAG and AAP were estimated by censoring methods. Genotyping was performed using the Multi-Ethnic Global Array (Illumina). Using GWAS summary statistics from the UK-Biobank, 29 significant and independent single nucleotide polymorphisms associated with age at voice break were extracted. Individual PRS were computed as the sum of risk alleles weighted by the effect size.

Results

The PRS was associated with AAG (β=0.01, P = 0.04) and AAP (β=0.185, P = 0.0004). In addition, boys within the 20% highest PRS experienced gonadarche and pubarche 0.55 and 0.67 years later than those in the lowest 20%, respectively (P = 0.013 and P = 0.007).

Conclusions

Genetic variants identified in large GWAS on age at VB significantly associate with age at testicular growth and pubic hair development, suggesting that these events share a genetic architecture across ethnically distinct populations.
Epidemiological evidence relating environmental smoke to COPD in lifelong non-smokers: a systematic review
Authors: Lee Peter N. , Forey Barbara A. , Coombs Katharine J. , Hamling Jan S. , Thornton Alison J.
Published: January 2020

Background: Some evidence suggests environmental tobacco smoke (ETS) might cause chronic obstructive pulmonary disease (COPD). We reviewed available epidemiological data in never smokers.

Methods: We identified epidemiological studies providing estimates of relative risk (RR) with 95% confidence interval (CI) for various ETS exposure indices. Confounder-adjusted RRs for COPD were extracted, or derived using standard methods.

Meta-analyses were conducted for each exposure index, with tests for heterogeneity and publication bias. For the main index (spouse ever smoked or nearest equivalent), analyses investigated variation in RR by location, publication period, study type, sex, diagnosis, study size, confounder adjustment, never smoker definition, and exposure index definition.

Results: Twenty-eight relevant studies were identified; nine European or Middle Eastern, nine Asian, eight American and two from multiple countries. Five were prospective, seven case-control and 16 cross-sectional. The COPD definition involved death or hospitalisation in seven studies, GOLD stage 1+ criteria in twelve, and other definitions in nine. For the main index, random-effects meta-analysis of 33 heterogeneous (p<0.001) estimates gave a RR of 1.20 (95%CI 1.08-1.34). Higher estimates for females (1.59,1.16-2.19, n=11) than males (1.29,0.94-1.76, n=7) or sexes combined (1.10,0.99-1.22, n=15 where sex-specific not available), and lower estimates for studies of 150+ cases (1.08,0.97-1.20, n=13) partly explained the heterogeneity. Estimates were higher for Asian studies (1.34,1.08-1.67, n=10), case-control studies (1.55,1.04-2.32, n=8), and COPD mortality or hospitalisation (1.40,1.12-1.74, n=11). Some increase was seen for severer COPD (1.29,1.10-1.52, n=7). Dose-response evidence was heterogeneous. Evidence for childhood (0.88,0.72-1.07, n=2) and workplace (1.12,0.77-1.64, n=4) exposure was limited, but an increase was seen for overall adulthood exposure (1.20,1.03-1.39, n=17). We discuss study weaknesses that may bias estimation of the association of COPD with ETS.

Conclusions: Although the evidence strongly suggests that ETS increases COPD, study weaknesses and absence of well-designed large studies preclude reliable effect estimation. More definitive evidence is required.
Cardiovascular, carcinogenic and reproductive effects of nicotine exposure: A narrative review of the scientific literature
Authors: Price Leonie R. , Martinez Javier
Published: January 2020

The emergence of new tobacco heating products and electronic nicotine delivery systems (ENDS) is changing the way humans are exposed to nicotine. The purpose of this narrative review is to provide a broad overview of published scientific literature with respect to the effects of nicotine on three key health-related areas: 1) cardiovascular risk, 2) carcinogenesis and 3) reproductive outcomes. These areas are known to be particularly vulnerable to the effects of cigarette smoke, and in addition, nicotine has been hypothesized to play a role in disease pathogenesis. Acute toxicity will also be discussed.

The literature to February 2019 suggests that there is no increased cardiovascular risk of nicotine exposure in consumers who have no underlying cardiovascular pathology. There is scientific consensus that nicotine is not a direct or complete carcinogen, however, it remains to be established whether it plays some role in human cancer propagation and metastasis. These cancer progression pathways have been proposed in models in vitro and in transgenic rodent lines in vivo but have not been demonstrated in cases of human cancer.

Further studies are needed to determine whether nicotine is linked to decreased fertility in humans. The results from animal studies indicate that nicotine has the potential to act across many mechanisms during fetal development. More studies are needed to address questions regarding nicotine exposure in humans, and this may lead to additional guidance concerning new ENDS entering the market.
Misannotation of multiple-nucleotide variants risks misdiagnosis
Authors: Wakeling Matthew N. , Laver Thomas W. , Colclough Kevin , Parish Andrew , Ellard Sian , Baple Emma L.
Published: January 2020

Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
The impact of birth-related injury and pain on breastfeeding outcomes
Authors: Bourdillon Katie , McCausland Tom , Jones Stephanie
Published: January 2020

Background

Reasons for premature discontinuation of breastfeeding are complex; a variety of social, psychological and physical factors may contribute to a deviation from a mother's breastfeeding plan.

Aims

To investigate how actual experiences of birth and breastfeeding differed from the mother's pre-birth intentions, and any subsequent perceived impact on breastfeeding experience.

Methods

Data was collected via an online survey of UK-based women (n=1 000).

Findings

Respondents faced a variety of challenges when breastfeeding, including nipple soreness and pain, concerns around milk insufficiency, and birth-related pain which impacted their ability to breastfeed comfortably. Predominantly, birth-related pain made breastfeeding difficult rather than preventing it, however 5% of mothers surveyed cited it as contributing to premature cessation of breastfeeding.

Conclusions

Pain relating to birth may be an under-considered factor in early cessation of breastfeeding. Considering the challenges experienced when establishing and maintaining breastfeeding, it is essential to consider the cumulative pain and discomfort experienced from all sources.
Effective hand hygiene—wash your hands and reduce the risk
Authors: Ridley Neesha
Published: January 2020

Neesha Ridley, Senior Lecturer, University of Central Lancashire, discusses the importance of hand hygiene in preventing healthcare-associated infections
Stepping out of your comfort zone
Authors: Emery Sophie
Published: January 2020

Sophie Emery, Student Children's Nurse at the University of Hertfordshire, reflects on her elective placement in Zambia
Celebrating nursing: why would I want to retire?
Authors: Zak Stephanie
Published: January 2020

Stephanie Zak reflects on her nursing career, from enrolled nurse to primary care nurse leader, and considers the role practice nurses can play in developing the future workforce
Short Communication: Two new species and new record of Psydrax Gaertn. (Rubiaceae: Vanguerieae) in Borneo
Authors: MAHYUNI RIDHA , CHIKMAWATI TATIK , ARIYANTI NUNIK SRI
Published: January 2020

Abstract. Mahyuni R, Chikmawati T, Ariyanti NS. 2019. Short Communication: Two new species and new record of  Psydrax Gaertn. (Rubiaceae: Vanguerieae) in Borneo. Biodiversitas 20: 2011-2015. Psydrax sabahensis Mahyuni and P. wongii Mahyuni are two new species endemic to Borneo proposed in this present study with descriptions, illustrations and map of distribution provided. Psydrax sabahensis has blades ovate to elliptic, with angle 60º to the midrib, tertiary venation conspicuous on both side, petiole length 10-13 mm long, inflorescence sub-umbellate and pedicels 23-27 mm long. Psydrax wongii has blade elliptic, with angle 45º to midrib, apex acuminate to caudate, secondary veins 3-4 pairs, tertiary venation inconspicuous on upper side and slightly wrinkled on lower surface. The presence of P. maingayi (Hook.f.) Bridson in Borneo, previously thought to be a Malay Peninsula endemic species, is also confirmed as a new record.
Rangeland conversion to dryland and its effects on species diversity and richness
Authors: Hasanpori REZA , Sepehry ADEL , Barani HOSSEIN
Published: January 2020

Abstract. Hasanpori R, Sepehry A, Barani H. 2019. Rangeland conversion to dryland and its effects on species diversity and richness. Biodiversitas 20: 2043-2047.  Species diversity and richness status in ecosystem is important in confront to environmental threats and is guidance in plant management. Due to increasing land use changes and destruction of rangelands in western Iran, this research was conducted to study the effects of land use change from rangeland to dryland on species diversity and richness of vegetation cover in three land uses of rangeland, dryland and abandoned dryland. Vegetation cover data were collected from established plots in each land use. Species diversity and richness were calculated in each land use by Simpson and Shannon indices and Menhinick and Margalef ones, respectively. Results showed that these indices are significantly different at 95% level in three land uses. The highest species diversity and richness indices were in rangeland and the least were in dryland. So, we found that four above measured indices, are illustrative and accurate enough to demonstrate differences between several land-use diversity and richness. Simplification on a dynamic and diverse ecosystem, and land conversion to dryland reduced plant species numbers in the new ecosystem, and simplify species composition, so simple dryland ecosystem would be fragile against environmental threats. Therefore to reduce unfavorable effects of land use changing, paying more attention to species diversity conservation must be a base to management decisions.
Short Communication: Analysis of the chemical constituents and micromorphology of Bauhinia scandens using SEM-EDS techniques
Authors: LIANAH LIANAH , IDRIS FATAH , KRISANTINI KRISANTINI
Published: January 2020

Abstract. Lianah L, Idris F, Krisantini K. 2019. Short Communication: Analysis of the chemical constituents and micromorphology of Bauhinia scandens using SEM-EDS techniques. Biodiversitas 20: 2055-2060. Some species of Bauhinia had a medicinal efficacy however the specific studies of Bauhinia scandens Willd. are relatively limited. Therefore this study analyzed the material and micromorphological characteristics of leaves, stems and roots of B. scandens using scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) to quantitatively assess the elements and explore its potential uses. Samples of fresh plant were taken from five locations in Indonesia, and the results showed similar snake-like stem morphology from two locations, while pilot ladder-like stem morphology was observed from the other three locations. The material analysis revealed the presence of carbon, oxygen, silicon, potassium, indium, tellurium, aluminum and iron in the samples. Interestingly, the stems did not contain indium and aluminum whereas iron were only found in the roots. Furthermore, the young leaves did not contain tellurium and silicon. The presence of indium which is potential as a cancer drug in B. scandens suggests promising uses of the plant for herbal medicines.
Detection of transovarial transmission of dengue virus in Aedes spp. (Diptera: Culicidae) from Brontokusuman Village, Yogyakarta, Indonesia
Authors: WINDYARAINI DILA HENING , MARSIFAH TITI , MUSTANGIN YAHYA , SOENARWAN HERY POERWANTO
Published: January 2020

Abstract. Windyaraini DH, Marsifah T, Mustangin Y, Poerwanto SH. 2019. Detection of transovarial transmission of dengue virus in Aedes spp. (Diptera: Culicidae) from Brontokusuman Village, Yogyakarta, Indonesia. Biodiversitas 20: 2061-2067. Dengue Hemorrhagic Fever (DHF) is an infectious vector-borne disease. It is caused by dengue virus infection through the vector of Aedes spp. Dengue virus can be transmitted transovarially from infected female mosquitoes to their eggs. The presence of transovarial transmission allows maintenance of serotypes of dengue virus in nature. Detection of transovarial transmissions can be used to predict disease outbreaks as an effort to control the dengue virus. Dengue control is generally carried out through control of dengue vectors (mosquitoes) with environmental management, the use of chemical agents (insecticides) and biological control. This study was conducted to determine the existence of transovarial (vertical) transmission, factors affecting it and the resistance status of Aedes spp. against cypermethrin insecticide (pyrethroid) in Brontokusuman Village, Mergangsan Sub-district of Yogyakarta, Indonesia. The study was conducted from September 2018 to February 2019 with larvae sampling in 100 houses. The adult Aedes spp. mosquitoes were used as the sample of immunohistochemical methods and bioassay to get the mosquito resistance status against cypermethrin. The transovarial transmission of dengue virus in Aedes spp. from Brontokusuman Village was found in 3 of 100 samples of Aedes spp. mosquitoes, and the TTI value (Transovarial Transmission Index) was 3%. The transovarial transmission is influenced by the density of the infected vectors, the condition of their eggs and the number of dengue cases. The bioassay test results showed that the resistance status of Aedes spp. can be presumed resistance against cypermethrin insecticide.
Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas
Authors: ANNA ROOSIANA DEVI  , Susilowati Ari , RATNA SETYANINGSIH
Published: January 2020

Abstract. Devi AR, Susilowati A, Setyaningsih R. 2019. Morphology, molecular identification, and pathogenicity of Vibrio spp. on blood clam (Anadara granosa) in Yogyakarta, Indonesia tourism beach areas. Biodiversitas 20: 2890-2896. Seafood is very popular among Indonesian people, especially in coastal areas. In Bantul Yogyakarta, blood clams have become one of tourist's favorite, either cooked or raw. Blood clams are filter feeders that cause the clams to be vulnerable to contamination of pathogenic bacteria that can cause foodborne disease, including Escherichia, Pseudomonas, and Vibrio. The 10-20% cases of foodborne disease transmitted through seafood caused by Vibrio spp. Three species of Vibrio can cause foodborne disease in humans, i.e., V. cholerae, V. parahaemolyticus, and V. vulnificus. The purpose of this study was to determine the character of Vibrio using morphological and molecular identification and pathogenicity on blood clam (Anadara granosa). Blood clams samples were collected from Depok, Goa Cemara, and Kwaru beaches in Bantul, Yogyakarta, Indonesia. Isolation of Vibrio spp. from blood clams was done using selective differential Thiosulfate Citrate bile salts sucrose (TCBS) culture medium. The morphological characters of the isolate colonies were determined based on the color, shape, texture, and size of the colony. Hemolysis test was also performed to evaluate the pathogenicity by using blood agar media. Molecular identification of Vibrio species was made using 16S rRNA sequence. Phylogenetic analysis was performed using Neighbor-Joining method in Mega X software. Samples for the analysis came from DNA sequences of this study and those from the GenBank database. Of the total 15 isolates obtained, four isolates showed positive β-hemolysis, namely, isolate P2S2 -1bH, P3S1-1aH, P2S1-1aK and P2S2-1aK, and one isolate had positive α-hemolysis (P3S2-1aK). Seven species of Vibrio were identified as V. algynolyticus, V. parahaemolyticus, V. diabolicus, V neocaledonicus, V. azureus, V. natrigens, and V. cholerae.
Characteristic of Tobacco mosaic virus isolated from cucumber and tobacco collected from East Java, Indonesia
Authors: LISTIHANI  , SRI HENDRASTUTI HIDAYAT  , SURYO WIYONO  , Damayanti Tri Asmira
Published: January 2020

Abstract. Listihani, Hidayat SH, Wiyono S, Damayanti TA. 2019. Characteristic of Tobacco mosaic virus isolated from cucumber and tobacco collected from East Java, Indonesia. Biodiversitas 20: 2937-2942. Tobacco mosaic virus (TMV) is a newly emerging virus infecting cucumbers in Java, Indonesia. The basic characters of the TMV isolated from cucumber need further study to investigate its differences with that from tobacco. Thus, the research aimed to study the character of both isolates based on their biological, symptomatology and nucleic acid of coat protein (CP) gene properties. The TMV isolates from both cucumber and tobacco were able to infect similar indicator plants with differing symptom expressions, especially on eggplant. Homology of nucleotide and amino acid of coat protein gene among isolates were about 90.3% and 91.0%, and homology to other isolates was about 87.6 to 93.8% and 89.3 to 96.8%, respectively. There were 17 amino acid differences in the CP gene which is presumed to differentiate those two isolates. Phylogenetic analysis CP gene sequences compared with corresponding isolates in GenBank showed the two isolates separated in different clades. The cucumber isolate from Kediri is closely related to tomato isolate from China in clade I, while tobacco isolate from Jember closely related to tobacco isolate from China in clade IIindicating the existence of two differ TMV variants. It will increase the difficulty to manage TMV in the fields.
Prediction of genetic gain in Ficus variegata progeny trial based on breeding value
Authors: HARYJANTO LILIEK , Prastyono Prastyono , Hadiyan Yayan , Susanto Mudji
Published: January 2020

Abstract. Haryjanto L, Prastyono, Hadiyan Y, Susanto M. 2019. Prediction of genetic gain in Ficus variegata progeny trial based on breeding value. Biodiversitas 20: 2994-2999. Prediction of genetic gain in Ficus variegata Blume progeny trial based on breeding values. The aim of this study was to estimate the breeding value based on components variance and genetic gain prediction of Ficus variegata Blume using REML/BLUP. A total of 17 families of Ficus variegata Blume were evaluated at three years after planting at progeny trial in Mangunan, Bantul, Yogyakarta laid out in Randomized Completely Block Design (RCBD). Estimation of variance family (height and diameter) were ± 5% of total variance. Narrow-sense individual heritability was moderate (0.27 and 0.21 respectively) indicated promising genetic improvement. Strong genetic correlation of height and diameter (rG=0.9) indicated that improving a trait will improving others. BLUP analysis for diameter trait showed that the best individual value from best family selection was appropriated with restriction 10 family and 5 individual per family and genetic gain prediction was 15.83% gave acceptable rate of inbreeding 2% per generation.
The potential of Mesangat Lake, East Kutai, Indonesia as an essential ecological area for habitat conservation of critically endangered Crocodylus siamensis
Authors: Sudrajat Sudrajat , HIKMA AMALIA SALEH
Published: January 2020

Abstract. Sudrajat, Saleh HA. 2019. The potential of Mesangat Lake, East Kutai, Indonesia as an essential ecological area for habitat conservation of critically endangered Crocodylus siamensis. Biodiversitas 20: 3126-3133. The Siamese crocodile, Crocodylus siamensis, is one of the most threatened reptile species in the world with IUCN Red List status of Critically Endangered. This study aims to investigate and assess the biogeophysical conditions of Mesangat Lake area, Indonesia as an essential ecological area for C. siamensis conservation outside biodiversity conservation areas. Data was collected through direct survey using spotlight technique at night, tracking, observation and interviews with local fishermen. The results showed that the biogeophysical conditions of Mesangat Lake habitat in Long Balau, Loah Toh and Abang areas still support C. siamensis population which was marked by the presence of its nests and the occurrence of 17 individuals with sizes between 30 and 50 cm in length. Habitat conditions in the form of lake waters had depths between 30-110 cm, low currents, and covered with aquatic plant species for resting, nesting and basking, as well as contained sufficient diversity of fish and other prey. A nest was also found in the form of mound of plants measuring ± 45 cm high and ± 75 cm wide which contained 20 eggs with an average length of ± 8.45 cm, an average width of ± 4.9 cm. Potential factors that threaten C. siamensis habitat included siltation of water bodies caused by invasive weeds, over-exploitation of fishes and conversion of lake land into plantations and/or agriculture lands. Based on the results of this study, it can be stated that Mesangat Lake has the potential to be designated as an essential ecological area of C. siamensis habitat. Through this strategy, it is hoped that there will be good collaboration between local government and concession rights holders, NGOs and local communities to participate in the conservation of C. siamensis. In the area of the lake, zoning can be classified into areas of nesting, closed areas, playing and sunbathing, limited fishing, recreation.
First record of the seagrass-boring shipworm Zachsia sp. (Bivalve: Teredinidae) in natural and transplanted Enhalus acoroides (Hydrocharitaceae) rhizomes in tropical Southwest Pacific
Authors: Asriani Nenni , Ambo-Rappe Rohani , Lanuru Mahatma
Published: January 2020

Seagrass ecosystems are under threat worldwide. Seagrass transplantation is one restoration approach which is has been tried with uneven success. While transplantation methods and oceanographic parameters have been investigated in attempts to understand the factors affecting transplant survival rate and seagrass transplantation success, little attention has been paid to the possible impact of pests. We observed borer molluscs in a seagrass Enhalus acoroides both from natural bed and transplant area. This is thought to be the first record from Indonesian waters of these bivalve molluscs of the genus Zachsia, family Teredinidae, the only mollusc genus known to bore into seagrass rhizomes. In a further eleven E. acoroides shoots (average length 10.5cm) we found between one and four calcareous burrows 2mm to 5mm in diameter inside the rhizome. Further research is required to determine the species present and its distribution in Indonesian waters as well as the true ecological impact of Zachsia sp. on seagrasses.
Student perceptions and experiences of charity on social media: the authenticity of offline networks in online giving
Authors: Dean Jon
Published: January 2020

Recent reports have cautioned that charities are behind the curve in taking advantage of the potential benefits of digital technologies and social media, a problem that particularly affects their engagement with young people. This article assesses the data from a series of focus groups, including a participatory digital element, with students and recent graduates (aged 18–25), examining participants’ current engagement with charity online. The focus groups show that while the right celebrity or organisational backing helps charity messages cut through, overall it is those causes and requests for donations that come through family and friends that are still the main drivers of young people’s engagement with charity on social media. Supporting findings from similar studies, this shows that, despite the global connectivity digital offers, we should think carefully about what can be expected from the charity–digital relationship, and the continued importance of existing offline relationships for students and new graduates.
Hyperspectral polarimetric imaging of the water surface and retrieval of water optical parameters from multi-angular polarimetric data
Authors: Gilerson Alexander , Carrizo Carlos , Ibrahim Amir , Foster Robert , Harmel Tristan , El-Habashi Ahmed , Lee ZhongPing , Yu Xiaolong , Ladner Sherwin , Ondrusek Michael
Published: January 2020

Total and polarized radiances from above the ocean surface are measured by a state-of-the-art snapshot hyperspectral imager. A computer-controlled filter wheel is installed in front of the imager allowing for recording of division-of-time Stokes vector images from the ocean surface. This system, to the best of our knowledge, for the first time provided a capability of hyperspectral polarimetric multi-angular measurements of radiances from above the water surface. Several sets of measurements used in the analysis were acquired from ocean platforms and from shipborne observations. Measurements made by the imager are compared with simulations using a vector radiative transfer (VRT) code showing reasonable agreement. Analysis of pixel-to-pixel variability of the total and polarized above-water radiance for the viewing angles of 20°–60° in different wind conditions enable the estimation of uncertainties in measurements of these radiances in the polarized mode for the spectral range of 450–750 nm, thus setting requirements for the quality of polarized measurements. It is shown that there is a noticeable increase of above-water degree of linear polarization (DoLP) as a function of the viewing angle, which is due both to the larger DoLP of the light from the water body and the light reflected from the ocean surface. Results of measurements and VRT simulations are applied for the multi-angular retrieval of the ratio of beam attenuation coefficient (

c

tot

) to absorption coefficient (

a

tot

) in addition to the other parameters such as absorption and backscattering coefficients retrieved from traditional unpolarized methods.
Symplectic ray tracing based on Hamiltonian optics in gradient-index media
Authors: Ohno Hiroshi
Published: January 2020

A method based on Hamiltonian optics for ray tracing through
gradient-index (GRIN) media is proposed. The ray equation that
describes light-ray paths can be written in the form of the
Hamiltonian equations. Although the Hamiltonian equations can be
numerically calculated using a finite-difference explicit method,
deviations from the exact equations are generally inevitable at
subsequent time steps. An optical Hamiltonian can be constructed of
two independent terms, i.e., one term dependent on position and the
other term dependent on momentum. The symplectic integrator is
applicable to such a separable optical Hamiltonian system and makes
the optical Hamiltonian equations form invariant at each time step of
numerical calculations. Accuracies of light-ray paths calculated using
the first-order symplectic ray tracing in GRIN lenses approximate
those calculated on the basis of the fourth-order Runge–Kutta
algorithm, which shows the promising potential of the
symplectic-ray-tracing method.
Metamaterial nonlinear and polarization-dependent bi-frequency THz switch
Authors: Sharifi Nahid , Granpayeh Nosrat
Published: January 2020

In this work, we propose a novel metamaterial structure with two concentric split-ring resonators. The splits are filled by photoconductive Si. Illuminating the structure using an oblique optical pump with a wavelength of 800 nm, in addition to the normal THz signal wave, excites the structure by varying the Si conductivity. Also, by changing the direction of the incident TE wave by 90°, the transmission frequency is changed. Therefore, the structure operates as a switch at two different windows using two different methods. The response time of the photoconductive switch is less than 3 ps. The substrate was replaced by a more cost-effective and flexible material, polyimide, to achieve even more exciting results in broadening the switching windows. Also, the response time of this switch is less than 1 ps. Finally, for verification of the simulation results, a circuit model of the photoconductive switch is proposed, and the results comply very well with the simulation results. The proposed switch can be used in fast optical systems and networks.
Berry-phase-based quantum gates assisted by transitionless quantum driving
Authors: Qi Shi-fan , Jing Jun
Published: January 2020

We propose a novel method for constructing geometric quantum gates
using three- or two-level systems, in which a controllable variable,
the detuning between the driving frequency and the atomic energy
spacing, is introduced to realize geometric transformations. In
particular, we have two instantaneous eigenstates with opposite
eigenvalues constituting a closed loop in the parameter space. The
accumulated dynamical phase is then exactly cancelled when the loop is
completed, which is beyond the traditional parallel-transport
restriction. We apply the transitionless quantum driving method to
enhance the speed and fidelity of geometric gates. Gate fidelity in
the presence of decoherence is also estimated.
Laser cooling of Yb3+:KYW
Authors: Cheng Long , Andre Laura B. , Salkeld Alexander J. , Andrade Luis H. C. , Lima Sandro M. , Silva Junior R. , Rytz Daniel , Rand Stephen C.
Published: January 2020

We report the first observation of laser cooling in Yb3+:KYW and validate the results by comparison with experiments in the well-studied material Yb3+:YAG. Radiation from a single-mode Ti:Al2O3 laser was used to achieve cooling of 1.5 K/W in 1% Yb:KYW at 1025 nm, comparing well with the reference material 3% Yb:YAG which cooled by 3.5 K/W at 1030 nm under open lab conditions. Experimental results for KYW crystals mounted on aerogels and doped with 1-20% Yb were in excellent agreement with the theoretical dependence of cooling power on the Yb absorption spectrum. Elimination of thermal conduction through the sample support structure was found to permit the attainment of lower temperatures and to simplify modeling of radiation balance conditions in self-cooled lasers with longitudinal thermal gradients. Contrary to the notion that more coolant ions yield higher cooling power, concentrations of Yb over 1% caused re-absorption of luminescence in KYW crystals, leading to a progressive red shift in the optimal cooling wavelength and the prevention of laser cooling altogether in a 20% sample at room temperature. The prospect of attaining radiation-balanced lasing in commercially-available tungstate crystals is evaluated.