bluuebunny/crossref_metadata_2025 huggingface dataset:
Trichome abundance, chlorophyll content and the spectral coefficient for light absorption of Trichodesmium slicks observed in the Southwestern Atlantic
Authors: Detoni Amália Maria Sacilotto , Ciotti Aurea Maria
Published: February 2020

Dense slicks of Trichodesmium were found in the shelf-break region in the Southwestern Atlantic during austral spring and autumn. A total of 14 slicks were sampled, and the absorption coefficients of phytoplankton (aph(λ)) indicated clear spectral features of phycobilin pigments. Although these samples showed low-degradation products and detrital importance, the chemotaxonomy, shape, and magnitude of aph(λ) indicated the importance of co-occurring species in the slicks. In addition to the difficulties of enumerating trichomes in situ, co-occurring species affect the expected chlorophyll-a (Chl-a) to trichome ratio, further complicating the detection of Trichodesmium by ocean colour remote sensing. Our results showed that trichome density could be predicted similarly by Chl-a and by aph(621), especially for trichome densities above 8000 trichomes L−1. The phycocyanin spectral feature is a potential source of quantitative information for the detection of Trichodesmium, but noninvasive techniques for quantifying the abundance of Trichodesmium in natural waters are necessary.
Effectiveness of Adjunctive Analgesics in Head and Neck Cancer Patients Receiving Curative (Chemo-) Radiotherapy: A Systematic Review
Authors: Lefebvre Tessa , Tack Laura , Lycke Michelle , Duprez Fréderic , Goethals Laurence , Rottey Sylvie , Cool Lieselot , Van Eygen Koen , Stubbs Brendon , Schofield Patricia , Pottel Hans , Boterberg Tom , Debruyne Philip
Published: February 2020

Objective

Our aim was to give an overview of the effectiveness of adjunctive analgesics in head and neck cancer (HNC) patients receiving (chemo-) radiotherapy.

Design

Systematic review.

Interventions

This systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. PubMed, Embase, Web of Science, the Cochrane Library, and ClinicalTrials.gov were searched for studies concerning “head neck cancer,” “adjunctive analgesics,” “pain,” and “radiotherapy.”

Outcome Measures

Pain outcome, adverse events, and toxicity and other reported outcomes, for example, mucositis, quality of life, depression, etc.

Results

Nine studies were included in our synthesis. Most studies were of low quality and had a high risk of bias on several domains of the Cochrane Collaboration tool. Only two studies comprised high-quality randomized controlled trials in which pregabalin and a doxepin rinse showed their effectiveness for the treatment of neuropathic pain and pain from oral mucositis, respectively, in HNC patients receiving (chemo-) radiotherapy.

Conclusions

More high-quality trials are necessary to provide clear evidence on the effectiveness of adjunctive analgesics in the treatment of HNC (chemo-) radiation-induced pain.
Developmental Trajectories of Cortical Thickness in Relation to Schizotypy During Adolescence
Authors: Derome Mélodie , Tonini Emiliana , Zöller Daniela , Schaer Marie , Eliez Stephan , Debbané Martin
Published: February 2020

Investigating potential gray matter differences in adolescents presenting higher levels of schizotypy personality traits could bring further insights into the development of schizophrenia spectrum disorders. Research has yet to examine the morphological correlates of schizotypy features during adolescence prospectively, and no information is available on the developmental trajectories from adolescence to adulthood. We employed mixed model regression analysis to investigate developmental trajectories of cortical thickness (CT) in relation to schizotypy dimensions in a cohort of 109 adolescents from the general population for whom MRI-scans were acquired over a 5-year period, culminating in a total of 271 scans. Structural data were processed with FreeSurfer software, statistical analyses were conducted using mixed regression models following a ROI-based approach, and schizotypy was assessed with the Schizotypal Personality Questionnaire (SPQ). Accelerated thinning was observed in the posterior cingulate cortex in relation to high levels of positive schizotypy, whereas high levels of disorganized schizotypy were associated with a similar trajectory pattern in the anterior cingulate cortex. The developmental course of CT in the prefrontal, occipital, and cingulate cortices differed between adolescents expressing higher vs lower levels of negative schizotypy. Participants reporting high scores on all schizotypy dimensions were associated with differential trajectories of CT in posterior cingulate cortex and occipital cortex. Consistently with prospective developmental studies of clinical risk conversion, the negative schizotypy dimension appears to constitute the most informative dimension for psychosis-related psychopathology, as its cerebral correlates in adolescents most closely overlap with results found in clinical high risk for psychosis studies.
CE: Brain Death: History, Updates, and Implications for Nurses
Authors: Milliken Aimee , Uveges Melissa
Published: February 2020

In 1968, the criteria for brain death were established by the Harvard Ad Hoc Committee. Despite what may appear to be unambiguous definitions, clinicians, ethicists, and the public have grappled with the concept of brain death since its inception. In light of recent public discourse on the topic, Harvard Medical School convened a conference to examine research and ethical inquiry conducted over the past 50 years related to death as defined by neurologic criteria. Drawing on the report produced by this conference, this article provides an overview of the development of brain death criteria, describes recent controversies and updates, and discusses implications of these criteria for nurses.
Case-Control Study of Paresthesia Among World Trade Center-Exposed Community Members
Authors: Marmor Michael , Thawani Sujata , Cotrina Maria Luisa , Shao Yongzhao , Wong Ericka S. , Stecker Mark M. , Wang Bin , Allen Alexander , Wilkenfeld Marc , Vinik Etta J. , Vinik Aaron I. , Reibman Joan
Published: February 2020

Objective:

To investigate whether paresthesia of the lower extremities following exposure to the World Trade Center (WTC) disaster was associated with signs of neuropathy, metabolic abnormalities, or neurotoxin exposures.

Methods:

Case-control study comparing WTC-exposed paresthesia cases with “clinic controls” (WTC-exposed subjects without paresthesias), and “community controls” (WTC-unexposed persons).

Results:

Neurological histories and examination findings were significantly worse in cases than controls. Intraepidermal nerve fiber densities were below normal in 47% of cases and sural to radial sensory nerve amplitude ratios were less than 0.4 in 29.4%. Neurologic abnormalities were uncommon among WTC-unexposed community controls. Metabolic conditions and neurotoxin exposures did not differ among groups.

Conclusions:

Paresthesias among WTC-exposed individuals were associated with signs of neuropathy, small and large fiber disease. The data support WTC-related exposures as risk factors for neuropathy, and do not support non-WTC etiologies.
Successful conservative management of a spontaneous intraperitoneal rupture of bladder diverticulum in a critical patient
Authors: Oh Seong Beom , Ahn Jung Hwan
Published: February 2020

Rationale:

A spontaneous rupture of the bladder diverticulum in an adult patient is extremely rare. The recommended treatment is surgery. However, some cases can be successfully treated with urinary catheterization, antibiotics, and/or percutaneous peritoneal drainage. In this case report, a spontaneous rupture of the bladder diverticulum was successfully treated non-surgically because it was deemed too risky for surgical intervention, such as non-ST segment elevation myocardial infarction (NSTEMI).

Patient concerns:

A 76-year-old man presented with abdominal pain, distention, diarrhea, and oliguria for 3 days and hypotension for 1 day with no history of trauma. The patient showed direct and rebound tenderness in the lower abdomen. Computed tomography revealed an intraperitoneal bladder rupture associated with the bladder diverticula. Electrocardiography, echocardiography, and elevated cardiac enzyme suggested NSTEMI.

Diagnoses:

A spontaneous rupture of the bladder diverticulum, NSTEMI, and suspected sepsis due to gastroenteritis or urinary infection.

Interventions:

The patient was treated conservatively with urinary catheterization and antibiotics for a bladder rupture and an infection. Percutaneous transluminal coronary angioplasty was performed for NSTEMI.

Outcomes:

The patient fully recovered without complications on hospitalization day 13.

Lessons:

Conservative management might be an alternative for a spontaneous intraperitoneal bladder rupture in some cases. However, close observation is required, and surgical intervention is the first option for a spontaneous intraperitoneal rupture of the bladder diverticulum.
Clinical Significance of CBS and CCL21 in Gallbladder Adenocarcinomas and Squamous Cell/Adenosquamous Carcinomas
Authors: Li Daiqiang , Yang Zhulin , Liu Ziru , Zou Qiong , Yuan Yuan
Published: February 2020

Gallbladder cancer (GBC) is a rare disease with high mortality. However, no biomarkers for the carcinogenesis, progression, prognosis, and early diagnosis are clinically available. This study investigated the expressions of cystathionine-β-synthase (CBS) and C-C chemokine receptor 7 (CCR7) protein and their clinical and pathologic significances in gallbladder squamous cell/adenosquamous carcinomas (SC/ASC) and adenocarcinomas (AC). CBS and chemokine ligand 21 (CCL21) expression was measured using immunohistochemistry in 69 SC/ASCs and 146 ACs. A significantly high percentage of patients with an age above 45 years, lymph node metastasis, and invasion was observed in the SCs/ASCs compared with ACs (P<0.05). Both AC and SC/ASC patients with positive CBS and CCL21 expression exhibited a high tumor-lymph node-metastasis stage, lymph node metastasis, and invasion compared with patients with negative CBS and CCL21 expression (P<0.05 or P<0.01). SC/ASC patients with positive CBS expression was prone to have a larger tumor size than those with negative expression (P<0.05). Positive CBS and CCL21 expression correlated with poor differentiation and larger tumor size in AC patients. Positive CBS and CCL21 are closely associated with a decreased overall survival in SC/ASC and AC patients (P<0.05 or P<0.01) and were independent factors for a poor-prognosis. Both CBS and CCL21 showed a good overall diagnostic performance for SC/ASC (AUC=0.742 and AUC=0.764, respectively) and AC (AUC=0.734 and AUC=0.718, respectively). In conclusion, positive CBS and CCL21 expression are closely associated with the clinical severity and poor prognosis in GBC, and can be a marker for the diagnosis of AC and SC/ASC type of GBC.
Complement Component C4d Deposition in the Placenta of Preeclampsia Patients and Renal Glomeruli in 1 Postpartum Renal Biopsy
Authors: Choi Song-Yi , Kim Kyung-Hee , Lee Mina , Yeo Min-Kyung , Kim Jae , Suh Kwang-Sun
Published: February 2020

Background:

The classic disorder of placental malperfusion is preeclampsia (PE), in which the kidney is also a target organ, leading to renal dysfunction. Although the precise pathogenesis of PE is unknown, increasing evidence suggests that PE is associated with complement dysregulation. The maternal immune response to an allogenic fetus and excessive activation of the complement system may both be involved in the pathogenesis of PE. C4d deposition is considered to be evidence of antibody-mediated rejection in an allograft. This study investigated a correlation between C4d expression in the placenta and clinicopathologic features of PE patients.

Materials and Methods:

Immunohistochemical staining for C4d was performed on placental tissue of PE patients (n=70) and normal pregnancy patients (n=30). Clinicopathologic features, such as maternal age and parity, placental weight, proteinuria, and histologic features of the placenta were evaluated. One PE patient who suffered from proteinuria after delivery received a renal biopsy.

Results:

C4d expression was demonstrated in syncytiotrophoblast of chorionic villi. The expression of C4d was significantly more frequent in the placenta with PE (50%) than in the placenta lacking complications (14.3%) (P=0.001). C4d expression was significantly accompanied by increased syncytial knots in PE (P=0.045). Among PE patients, C4d expression was significantly correlated with low placental weight (P=0.001) and high proteinuria (P=0.018, Mann-WhitneyUtest). Renal biopsy of a PE patient after delivery also showed deposition of C4d along the glomerular capillary walls.

Conclusions:

C4d may play an important role in placental tissue injury and in renal complications in PE.
Clinic-Based Pediatric Disclosure Intervention Trial Improves Pediatric HIV Status Disclosure in Ghana
Authors: Paintsil Elijah , Kyriakides Tassos C. , Antwi Sampson , Renner Lorna , Nichols Justin S. , Amissah Kofi , Kusah Jonas T. , Alhassan Amina , Ofori Irene P. , Catlin Ann C. , Gan Geliang , Lartey Margaret , Reynolds Nancy R. ,   on behalf of the Sankofa Study Team
Published: February 2020

Background:

Disclosing HIV status to HIV-positive children is a major challenge facing families and health care providers. Despite recommendations for disclosure, rates remain low. We tested whether a pediatric HIV disclosure intervention delivered as an integral component of routine HIV health care in Ghana would improve disclosure to children.

Methods:

Dyads of HIV-infected children aged 7–18 years and their caregivers were enrolled from 2 HIV clinics in Accra and Kumasi, Ghana. The sites were randomly assigned to one of the 2 intervention arms to avoid treatment contamination between intervention and control participants. Trained interventionist used theory-guided therapeutic communication and personalized interaction to promote disclosure. Disclosure outcomes were measured at 12-week intervals. All analyses were completed using a modified intention-to-treat approach.

Results:

We enrolled 446 child–caregiver dyads (N = 240 intervention group; N = 206 control group); 52% of the children were boys, mean age 9.78 (±2.27) years. For disclosure at 1 year, a better overall treatment effect was observed (P < 0.001). Children in the treatment group had greater disclosure at each time point (P < 0.001) and a higher proportion of them had been disclosed to by 1 year (51.4% vs. 16.2%; P < 0.001; un-adjusted hazard ratio = 3.98: 95% confidence interval: 2.63 to 6.03) and 3 years (71.3% vs. 34.0%; unadjusted hazard ratio = 4.21: 95% confidence interval: 3.09 to 5.72). In the multivariate Cox model, factors associated with disclosure were treatment group (P < 0.001), children <11 years of age (P < 0.001), HIV-infected caregivers (P = 0.015), and caregiver's with greater education (P = 0.022).

Conclusions:

This practical clinic-based disclosure intervention shows excellent promise as a means of improving HIV pediatric disclosure outcomes.
The Monobloc Distraction With Facial Bipartition
Authors: Goel Pedram , Munabi Naikhoba C.O. , Nagengast Eric S. , Williams Madeleine S. , Fahradyan Artur , Urata Mark M.
Published: February 2020

Background

Although combined monobloc facial bipartition with distraction (MFBD) may simultaneously correct multiple facial dimensions in patients with syndromic craniosynostoses, complication risks limit its use. This study reassesses MFBD complications and outcomes to compare safety and efficacy to monobloc distraction (MD) and facial bipartition (FB) alone.

Methods

A retrospective review of MFBD, MD, and FB cases for 10 years at a tertiary children's hospital was performed. Patient demographics and surgical variables were compared between cohorts. Distraction distance was compared between MFBD and MD. Correction of interdacryon distance in MFBD compared with FB was measured on preoperative and postoperative computed tomographic scans. SPSS 17 was used for data analysis.

Results

Twenty-two total patients, 11 MFBD, 4 MD, and 7 FB, met the inclusion criteria. Three MFBD (27.3%) patients experienced complications, including 1 osteomyelitis and 2 hardware displacements. One MD patient (25%) experienced a postoperative complication consisting of a wound infection. Three FB patients (42.9%) experienced either cerebrospinal fluid leak, seroma, mucocele, hardware exposure, and/or orbital dystopia (n = 1 each). Patients with MFBD had significantly longer intensive care unit stay (P ≤ 0.05), but no difference in hospital stay (P = 0.421). Mean distraction length was similar between MFBD and MD (P = 0.612). There was no significant difference in final (P = 0.243) or change (P = 0.189) in interdacryon distance between MFBD and FB patients.

Conclusions

In our experience, MFBD has similar complication rates compared with MD and FB alone. Given equivalent safety and postoperative correction of facial dimensions, MFBD could be more widely considered for select patients.
Late-Onset Infection of Resorbable Plates After Multiple Facial Fractures
Authors: Ueki Shoya , Rikimaru Hideaki , Rikimaru-Nishi Yukiko , Midorikawa Mari , Kiyokawa Kensuke
Published: February 2020

In recent years, a variety of resorbable plates have been used for craniofacial fractures. The authors report a case of plate infection that occurred more than 1 year after surgery and was difficult to distinguish from a foreign body reaction. A 19-year-old male suffered fractures of the right zygomatic bone, orbital floor, and left maxilla in a motorcycle accident. Reduction was performed using resorbable plates at 7 days after injury. The postoperative course was good. However, the patient presented 396 days after surgery with redness/swelling of the right upper eyelid and right cheek pain. There were no systemic signs of infection such as fever. A foreign body reaction to the plate was suspected. After 1 week, swelling of the patient's upper eyelid was worse, and the remaining resorbable plate was removed via a skin incision. Swelling subsequently extended to the right cheek and upper gingiva, and all plates were removed under general anesthesia on the 418th day after the first operation. The swelling subsided after removal of the plates. Pathological examination revealed neutrophil infiltration and Staphylococcus hominis was detected by bacterial culture, leading to a diagnosis of late-onset plate infection. This coagulase-negative staphylococcus usually causes infection in neonates and immunocompromised individuals. Postoperative complications of resorbable plates include foreign body reaction and infection, which are difficult to differentiate clinically. Removing the foreign body is the principal technique for obvious wound infection. A foreign body reaction with subcutaneous fluid retention is slow to heal. Therefore, early plate removal is also recommended.
Sequential Changes of NLRP3 Inflammasome Activation in Sepsis and its Relationship With Death
Authors: Garnacho-Montero José , Palacios-García Inmaculada , Díaz-Martín Ana , Gutiérrez-Pizarraya Antonio , López-Sánchez José M. , Gómez Elísabet Alcocer , Cordero Mario D.
Published: February 2020

Introduction:

Inflammasomes are recognized as key components of the innate immune response in sepsis. We aimed to describe the transcriptional expression of nucleotide-binding domain, leucine-rich repeat–containing receptor, pyrin domain–containing-3 (NLRP3), and serum interleukin-1β (IL-1 β) in critically ill patients, their changes over the first week and their prognostic value in septic patients.

Methods:

Prospective study including patients with sepsis based on Sepsis-3 definitions and a control group of critically ill patients without sepsis. We measured the circulating levels of IL-1β as well as the transcriptional expression of NLRP3 at admission and on days 3 and 7. Caspase-1 and caspase-3 activation was analyzed in a matched cohort of patients with septic shock (four dead and four survivors).

Results:

Fifty-five septic patients and 11 non-septic patients were studied. Levels on day 0 and 3 of IL-1 β and NLRP3 inflammasome expression were significantly higher in patients with sepsis than in controls. NLRP3 was significantly higher in septic patients who survived at day 7 without significant difference between survivors and non-survivors at baseline and on day 3. In survivors, an increased caspase-1 protein expression with reduced expression caspase-3 was observed with the opposite pattern in those who died.

Conclusions:

NLRP3 is activated in critically ill patients but this up-regulation is more intense in patients with sepsis. In sepsis, a sustained NLRP3 activation during the first week is protective and sepsis. An increased caspase-1 protein expression with reduced expression caspase-3 is the pattern observed in septic shock patients who survive.
High-activity Classical and Alternative Complement Pathway Genotypes—Association With Donor-specific Antibody-triggered Injury and Renal Allograft Survival
Authors: Mező Blanka , Reindl-Schwaighofer Roman , Eskandary Farsad , Heinzel Andreas , Wahrmann Markus , Doberer Konstantin , Heilos Andreas , Bond Gregor , Kläger Johannes , Kozakowski Nicolas , Haslacher Helmuth , Oberbauer Rainer , Viklický Ondřej , Hrubá Petra , Halloran Philip F. , Rusai Krisztina , Prohászka Zoltán , Böhmig Georg A.
Published: February 2020

Background.

Complement may contribute to donor-specific antibody (DSA)-triggered transplant injury. Here, we investigated whether the intrinsic strength of classical pathway and alternative pathway (AP) relates to the pathogenicity of DSA.

Methods.

Classical pathway and AP high-activity genotypes were defined according to C4 gene copy number and the presence of functional polymorphisms in C3 (C3102G), factor B (fB32R), and factor H (fH62V) genes. Associations of these genotypes with blood complement profiles and morphologic/molecular rejection features were evaluated in a cohort of 83 DSA-positive patients (antibody-mediated rejection [AMR], n = 47) identified upon cross-sectional screening of 741 kidney allograft recipients ≥180 days posttransplantation. Associations with long-term graft survival were evaluated in a larger kidney transplant cohort (n = 660) not enriched for a specific type of rejection.

Results.

In the cohort of DSA-positive subjects, the number of C4 gene copies was related to C4 protein levels in serum and capillary C4d staining, but not AMR activity. Patients with a high-activity AP complotype, which was associated with complement consumption in serum, showed enhanced microcirculation inflammation (median glomerulitis plus peritubular capillaritis score, 2 [interquartile range, 0–4 versus 1 0–2]; P = 0.037). In the larger transplant cohort, this complotype was associated with a slightly increased risk of graft loss (hazard ratio, 1.52; 95% confidence interval, 1.02-2.25; P = 0.038 and multivariable Cox model, 1.55; 1.04-2.32; P = 0.031).

Conclusions.

Our study suggests a contribution of complement genetics to the phenotypic presentation of AMR. Future studies will have to clarify whether a possible association of AP strength with graft survival relates to enhanced antibody-triggered injury.
Weak predation strength promotes stable coexistence of predators and prey in the same chain and across chains
Authors: Wang Lin , Liu Yan-Ping , Wang Rui-Wu
Published: February 2020

The mechanisms of species coexistence make ecologists fascinated, although theoretical work show that omnivory can promote coexistence of species and food web stability, it is still a lack of the general mechanisms for species coexistence in the real food webs, and is unknown how omnivory affects the interactions between competitor and predator. In this work, we first establish an omnivorous food web model with a competitor based on two natural ecosystems (the plankton community and fig-fig wasp system). We analyze the changes of both food web structure and stability under the different resource levels and predation preference of the generalist/top predator. The results of model analyses show that weak predation strength can promote stable coexistence of predators and prey. Moreover, evolutionary trend of food web structure changes with the relative predation strength is more diversity than the relative competition strength, and an integration of both omnivory, increased competition, top-down control and bottom-up control can promote species diversity and food web stability. Our theoretical predictions are consistent with empirical data in the plankton community: the lower concentration of nutrient results in a more stable population dynamics. Our theoretical work could enrich the general omnivorous theory on species coexistence and system stability in the real food webs.
IntracellularStaphylococcus aureusemploys the cysteine protease staphopain A to induce host cell death in epithelial cells
Authors: Stelzner Kathrin , Hertlein Tobias , Sroka Aneta , Moldovan Adriana , Paprotka Kerstin , Kessie David , Mehling Helene , Potempa Jan , Ohlsen Knut , Fraunholz Martin J. , Rudel Thomas
Published: February 2020

Staphylococcus aureusis a major human pathogen, which can invade and survive in non-professional and professional phagocytes. Intracellularity is thought to contribute to pathogenicity and persistence of the bacterium. Upon internalization by epithelial cells, cytotoxicS. aureusstrains can escape from the phagosome, replicate in the cytosol and induce host cell death. Here, we identified a staphylococcal cysteine protease to induce cell death by intracellularS. aureusafter translocation into the host cell cytoplasm. We demonstrated that loss of staphopain A function leads to delayed onset of host cell death and prolonged intracellular replication ofS. aureusin epithelial cells. Overexpression of staphopain A in a non-cytotoxic strain facilitated intracellular killing of the host cell even in the absence of detectable intracellular replication. Moreover, staphopain A contributed to efficient colonization of the lung in a mouse pneumonia model. Our study suggests that staphopain A is utilized byS. aureusto mediate escape from the host cell and thus contributes to tissue destruction and dissemination of infection.

Author Summary

Staphylococcus aureusis a well-known antibiotic-resistant pathogen that emerges in hospital and community settings and can cause a variety of diseases ranging from skin abscesses to lung inflammation and blood poisoning. The bacterium asymptomatically colonizes the upper respiratory tract and skin of about one third of the human population and takes advantage of opportune conditions, like immunodeficiency or breached barriers, to cause infection. AlthoughS. aureusis not regarded as a professional intracellular bacterium, it can be internalized by human cells and subsequently exit the host cells by induction of cell death, which is considered to cause tissue destruction and spread of infection. The bacterial virulence factors and underlying molecular mechanisms involved in the intracellular lifestyle ofS. aureusremain largely unknown. We identified a bacterial cysteine protease to contribute to host cell death mediated by intracellularS. aureus. Staphopain A induced killing of the host cell after translocation of the pathogen into the cell cytosol, while bacterial proliferation was not required. Further, the protease enhanced survival of the pathogen during lung infection. These findings reveal a novel, intracellular role for the bacterial protease staphopain A.
Revisiting reptile home ranges: moving beyond traditional estimators with dynamic Brownian Bridge Movement Models
Authors: Silva Inês , Crane Matt , Marshall Benjamin Michael , Strine Colin Thomas
Published: February 2020

Animal movement, expressed through home ranges, can offer insights into spatial and habitat requirements. However, home range estimation methods vary, directly impacting conclusions. Recent technological advances in animal tracking (GPS and satellite tags), have enabled new methods for home range estimation, but so far have primarily targeted mammal and avian movement patterns. Most reptile home range studies only make use of two older estimation methods: Minimum Convex Polygons (MCP) and Kernel Density Estimators (KDE), particularly with the Least Squares Cross Validation (LSCV) and reference (href) bandwidth selection algorithms. The unique characteristics of reptile movement patterns (e.g.low movement frequency, long stop-over periods), prompt an investigation into whether newer movement-based methods –such as dynamic Brownian Bridge Movement Models (dBBMMs)– are applicable to Very High Frequency (VHF) radio-telemetry tracking data. To assess home range estimation methods for reptile telemetry data, we simulated animal movement data for three archetypical reptile species: a highly mobile active hunter, an ambush predator with long-distance moves and long-term sheltering periods, and an ambush predator with short-distance moves and short-term sheltering periods. We compared traditionally used home range estimators, MCP and KDE, with dBBMMs, across eight feasible VHF field sampling regimes for reptiles, varying from one data point every four daylight hours, to once per month. Although originally designed for GPS tracking studies, we found that dBBMMs outperformed MCPs and KDEhrefacross all tracking regimes, with only KDE LSCV performing comparably at some higher-frequency sampling regimes. The performance of the LSCV algorithm significantly declined with lower-tracking-frequency regimes, whereas dBBMMs error rates remained more stable. We recommend dBBMMs as a viable alternative to MCP and KDE methods for reptile VHF telemetry data: it works under contemporary tracking protocols and provides more stable estimates, improving comparisons across regimes, individuals and species.
Polynomial Phylogenetic Analysis of Tree Shapes
Authors: Liu Pengyu , Biller Priscila , Gould Matthew , Colijn Caroline
Published: February 2020

Abstract

Phylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes is a challenging aspect of comparing phylogenetic trees as there are few tools to describe tree shapes in a quantitative, accurate, comprehensive and easy-to-interpret way. Current methods to compare tree shapes are often based on scalar indices reflecting tree imbalance, and on frequencies of small subtrees. In this paper, we present tree comparisons and applications based on a polynomial that fully characterizes trees. Polynomials are important tools to describe discrete structures and have been used to study various objects including graphs and knots. There are also polynomials that describe rooted trees. We use tree-defining polynomials to compare tree shapes randomly generated by simulations and tree shapes reconstructed from data. Moreover, we show that the comparisons can be used to estimate parameters and to select the best-fit model that generates specific tree shapes.
Weighted minimizer sampling improves long read mapping
Authors: Jain Chirag , Rhie Arang , Zhang Haowen , Chu Claudia , Koren Sergey , Phillippy Adam
Published: February 2020

Motivation

In this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence comparison. This technique yields a sub-linear representation of sequences, enabling their comparison in reduced space and time. A key property of the minimizer technique is that if two sequences share a substring of a specified length, then they can be guaranteed to have a matching minimizer. However, because thek-mer distribution in eukaryotic genomes is highly uneven, minimizer-based tools (e.g., Minimap2, Mashmap) opt to discard the most frequently occurring minimizers from the genome in order to avoid excessive false positives. By doing so, the underlying guarantee is lost and accuracy is reduced in repetitive genomic regions.

Results

We introduce a novel weighted-minimizer sampling algorithm. A unique feature of the proposed algorithm is that it performs minimizer sampling while taking into account a weight for eachk-mer; i.e, the higher the weight of ak-mer, the more likely it is to be selected. By down-weighting frequently occurringk-mers, we are able to meet both objectives: (i) avoid excessive false-positive matches, and (ii) maintain the minimizer match guarantee. We tested our algorithm, Winnowmap, using both simulated and real long-read data and compared it to a state-of-the-art long read mapper, Minimap2. Our results demonstrate a reduction in the mapping error-rate from 0.14% to 0.06% in the recently finished human X chromosome (154.3 Mbp), and from 3.6% to 0% within the highly repetitive X centromere (3.1 Mbp). Winnowmap improves mapping accuracy within repeats and achieves these results with sparser sampling, leading to better index compression and competitive runtimes.

Contact

adam.phillippy@nih.gov

Availability

Winnowmap is built on top of the Minimap2 codebase (Li, 2018) and is available athttps://github.com/marbl/winnowmap.
Crystal structure of poly[(μ3-4-amino-1,2,5-oxadiazole-3-hydroxamato)thallium(I)]
Authors: Safyanova Inna S. , Bondar Oksana A. , Pavlishchuk Anna V. , Omelchenko Iryna V. , Iskenderov Turganbay S. , Kalibabchuk Valentina A.
Published: February 2020

The title compound represents the thallium(I) salt of a substituted 1,2,5-oxadiazole, [Tl(C3H3N4O3)]
n
, with amino- and hydroxamate groups in the 4- and 3- positions of the oxadiazole ring, respectively. In the crystal, the deprotonated hydroxamate group represents an intermediate between the keto/enol tautomers and forms a five-membered chelate ring with the thallium(I) cation. The coordination sphere of the cation is augmented to a distorted disphenoid by two monodentately binding O atoms from two adjacent anions, leading to the formation of zigzag chains extending parallel to the b axis. The cohesion within the chains is supported by π–π stacking [centroid–centroid distance = 3.746 (3) Å] and intermolecular N—H...N hydrogen bonds.
(3S,5R,6S)-Diphenylmethyl 1-oxo-6-bromopenicillanate
Authors: Soundararajan Krishnan , Sethuraman Velusamy , Thanigaimani Kaliyaperumal
Published: February 2020

In the title compound, C21H20BrNO4S, a key intermediate in the synthesis of the widely used β-lactamase inhibitor tazobactam, the five-membered thiazolidine ring adopts an envelope conformation and the four-membered azetidine ring is in a distorted planar conformation. The crystal structure features C—H...O hydrogen bonds and a weak C—H...π interaction.
Citation behavior of Pondicherry University faculty in digital environment: a survey
Authors: Singson Mangkhollen , Sunny Stephy K. , Thiyagarajan S. , Dkhar Valerie
Published: February 2020

Purpose

The purpose of this paper is to understand the citation behavior of Pondicherry University faculty with a focus on their recent publication experience, indexed in Scopus. The paper endeavors to gain an insight into their pattern of citation of scientific papers and attempts to understand the underlying motive in doing so especially in an era where information resources have transitioned from print to digital.

Design/methodology/approach

The study adopted a judgmental sample consisting of 100 selected faculty members whose recent papers were indexed by Scopus database. A pre-defined questionnaire consisting of demographic profile and 23 items on citation trust and authority statements of citing sources was self-administered to them.

Findings

The findings of the study indicate that the citation behavior of faculty in Pondicherry University is complex and multi-faceted. Although majority of the faculty depicted an inclination toward normative citation behavior (concerned with the intellectual content of the work), there are others who displayed social constructivist (concerned with the social aspects of the work) citation behavior as well. However, in spite of the differences observed in the citation behavior of the faculty, it was observed that they remained traditional while making trust decisions even in the digital era. Finally, findings suggest no statistical significant difference when it comes to variables, such as gender and discipline in the citation behavior of the faculty.

Originality/value

Given the ever-increasing importance of citation in judging the quality of research journals, in ranking institutions and in determining the efficacy of faculty in India, author-based approach of understanding citer motivation definitely carry research value.
Challenge or opportunity of climate financial fragmentation
Authors: Liang Chao , Liu Bai
Published: February 2020

Purpose

This study aims to investigate the environmental effects of climate financial fragmentation in the form of emerging multilateral institutions.

Design/methodology/approach

Among the countries that have economic relations with China, those involved in climate finance cooperation are taken as the experimental group, and those not involved in other areas are taken as a control group. Using system generalized method of moments regression, the difference-in-differences method is used to test the environmental effects of climate finance cooperation of emerging multilateral institutions. In this way, this study explores the financial and trade mechanisms of cooperation among emerging multilateral institutions.

Findings

The results of this empirical study show that the cooperation of emerging multilateral institutions has a positive impact on the environment. Research results further reveal the financial and trade mechanisms of climate finance cooperation projects. When the invested countries are more likely to obtain international capital, environmental effects will be greater. However, trade intimacy could inhibit the improved environmental effects.

Originality/value

This research is one of the few studies to test the environmental effects of climate financial fragmentation empirically. This study provides a better understanding of the multilateral cooperation of emerging economic entities and China’s climate finance policy, thus providing evidence for the collaborative governance of global climate finance.
Scale up predictive models for early detection of at-risk students: a feasibility study
Authors: Cui Ying , Chen Fu , Shiri Ali
Published: February 2020

Purpose

This study aims to investigate the feasibility of developing general predictive models for using the learning management system (LMS) data to predict student performances in various courses. The authors focused on examining three practical but important questions: are there a common set of student activity variables that predict student performance in different courses? Which machine-learning classifiers tend to perform consistently well across different courses? Can the authors develop a general model for use in multiple courses to predict student performance based on LMS data?

Design/methodology/approach

Three mandatory undergraduate courses with large class sizes were selected from three different faculties at a large Western Canadian University, namely, faculties of science, engineering and education. Course-specific models for these three courses were built and compared using data from two semesters, one for model building and the other for generalizability testing.

Findings

The investigation has led the authors to conclude that it is not desirable to develop a general model in predicting course failure across variable courses. However, for the science course, the predictive model, which was built on data from one semester, was able to identify about 70% of students who failed the course and 70% of students who passed the course in another semester with only LMS data extracted from the first four weeks.

Originality/value

The results of this study are promising as they show the usability of LMS for early prediction of student course failure, which has the potential to provide students with timely feedback and support in higher education institutions.
Evaluating the use of data-based offender profiling by researchers, practitioners and investigative journalists to address unresolved serial homicides
Authors: Yaksic Enzo
Published: February 2020

Purpose

The purpose of this article is to improve the use of evidence-based practice and research utilization in the offender profiling process. The use of offender profiling has been met with increasing resistance given its exaggerated accuracy. The “Investigative Journalist/Expert Field Micro Task Force” model, a collaborative method that incorporates offender profiling and is designed to address unresolved serial homicides, is introduced and evaluated alongside recommendations on attaining adherence.

Design/methodology/approach

The model was field tested in 17 instances. The measures used by the Federal Bureau of Investigation to gauge the usefulness of their case consultations, whether their input helped catch the offender, offer new leads, move the case forward, provide new avenues or give new ideas, were used to evaluate the model.

Findings

The model established likely patterns of serial murder activity among strangulations of women in Chicago, Cleveland, and Panama and resulted in convictions of suspects in Louisiana and Kansas City. This model is valuable when used to parse modern-day offenders from those who committed unresolved homicides as the latter display different behaviors that can make investigations difficult endeavors. Results from the field tests mirror those from the literature in that profiling alone did not result in the capture of serial killers. Instead, profiling was used in conjunction with other efforts and mainly as a means to keep the investigation moving forward.

Originality/value

Unresolved homicides are at a point of crisis and represent a significant but largely unaddressed societal problem. The success of this model may compel law enforcement to restore faith in offender profiling.
An Entrepreneurial Management System for established companies
Authors: Osiyevskyy Oleksiy , Radnejad Amir Bahman , MahdaviMazdeh Hossein
Published: February 2020

Purpose

The article introduces the Entrepreneurial Management System (EMS), which delineates a strategic process within an organizational context that is aimed at encouraging and supporting the pursuit of opportunities that have the potential to create value through innovative strategic actions. It is designed to stimulate entrepreneurial thinking and corporate venturing at all levels.

Design/methodology/approach

The authors offer an approach to organization-wide continuous innovation that incorporates proven concepts from existing research with lessons learned from the authors’ research analysis and consulting experience in helping large and medium companies across different industries and markets to establish effective entrepreneurial management.

Findings

Given the spectre of constant disruption from new technologies or business models, management teams will be judged on how they proactively respond to these challenges by turning them into value-creating opportunities.

Practical implications

Multidisciplinary teams allow employees to become familiar with other domains and see possible solutions, share their problems and ideas and vet their insights with the input of colleagues.

Originality/value

An Entrepreneurial Management System allows a firm to "internalize" the marketplace’s evolutionary processes so that a company can generate, develop and implement ideas that will have value for customers. It should be a clear decision for all of today’s business leaders and investors to have an implementation plan to ensure continuous innovation.
Manipulation of sensory characteristics and volatile compounds in strawberry fruit through the use of isolated wavelengths of light
Authors: Campbell Sean M. , Sims Charles A. , Bartoshuk Linda M. , Colquhoun Thomas A. , Schwieterman Michael L. , Folta Kevin M.
Published: February 2020

Consumers consistently note that there is room for improvement in the flavor of commercial strawberries. Fruit flavor and aroma are affected by both genetics and environment. This work tests the hypothesis that sensory quality may be manipulated using postharvest light treatments. Individual detached fruits representing two different cultivars received a 24‐hr treatment of 100 µmol m−2 s−1 blue LED light while the control was kept in complete darkness. Following treatment, samples were analyzed for flavor volatiles, sugars, acids, firmness, and sensory differences in human trials. Fruits were rated for overall liking, texture, sweetness, sourness, and overall strawberry flavor intensity (OSFI) on the sensory and hedonic versions of the global intensity scale (GIS). A positive treatment effect was observed for “Strawberry Festival” fruit for the overall liking rating. A triangle test revealed a significant treatment effect, as light‐treated fruit tested higher in many flavor volatiles including those known to contribute to sweetness in strawberries. Levels of several volatiles were consistently higher in the treated fruit across all four harvests: acetic acid hexyl ester, butanoic acid octyl ester, methyl isovalerate, and pentanoic acid ethyl ester. The results show that postharvest light treatment can be used to modulate sensory quality of fruit, perhaps offering a means to complement genetic efforts in fruit flavor and aroma improvement.

Practical Application

The results indicate that it may be possible to increase the sensory quality of strawberry fruits using an inexpensive and noninvasive light treatment. Light may be applied during transport or storage to improve fruit quality. This concept could also be extended into other realms of storage, such as residential and commercial refrigeration, further increasing the quality impact of the approach.
Variability and effectiveness of comparator group interventions in smoking cessation trials: a systematic review and meta‐analysis
Authors: Black Nicola , Eisma Maarten C. , Viechtbauer Wolfgang , Johnston Marie , West Robert , Hartmann‐Boyce Jamie , Michie Susan , de Bruin Marijn
Published: February 2020

Aims

To examine variability and effectiveness of interventions provided to comparator (control) groups in smoking cessation trials.

Methods

Systematic review with meta‐analysis of randomized controlled trials (RCTs) of behavioral interventions for smoking cessation, with or without stop‐smoking medication. We searched the Cochrane Tobacco Addiction Group Specialized Register for RCTs with objective outcomes measured at ≥ 6 months. Study authors were contacted to obtain comprehensive descriptions of their comparator interventions. Meta‐regression analyses examined the relationships of smoking cessation rates with stop‐smoking medication and behavior change techniques.

Results

One hundred and four of 142 eligible comparator groups (n = 23 706) had complete data and were included in analyses. There was considerable variability in the number of behavior change techniques delivered [mean = 15.97, standard deviation (SD) = 13.54, range = 0–45] and the provision of smoking cessation medication (43% of groups received medication) throughout and within categories of comparator groups (e.g. usual care, brief advice). Higher smoking cessation rates were predicted by provision of medication [B = 0.334, 95% confidence interval (CI) = 0.030–0.638, P = 0.031] and number of behavior change techniques included (B = 0.020, 95% CI = 0.008–0.032, P < 0.001). Modelled cessation rates in comparator groups that received the most intensive support were 15 percentage points higher than those that received the least (23 versus 8%).

Conclusions

Interventions delivered to comparator groups in smoking cessation randomized controlled trials vary considerably in content, and cessation rates are strongly predicted by stop‐smoking medication and number of behavior change techniques delivered.