bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diel vertical distribution and life history characteristics ofTropodiaptomus simplexand its importance in the diet ofStolothrissa tanganicae, Kigoma, Tanzania
Authors: Mgana H. F. , Herzig A. , Mgaya Y. D. 
Published: October 2017

Tropocyclops simplex abundance, diel distribution and the impact of the planktivore fish Stolothrissa tanganicae on the T. simplex population were studied at a deep-water site in Kigoma Bay, Lake Tanganyika during the wet period (October 2008–February 2009). The top 40 m were examined using discrete depth samples, filtered through a 40-μm mesh. Ovigerous and copepodids of Tropodiaptomus simplex exhibited a very clear diel vertical migration. Ovigerous females of Tropodiaptomus were negligibly low in the 0–30 m depth during the day, while at night they stayed above 20 m. Tropodiaptomus nauplii did not show any clear diel vertical migration. The contribution of adults, copepodite and nauplii stages to the total numbers of Tropodiaptomus simplex was 8.2, 8.6 and 83.2%, respectively. Stolothrissa tanganicae stomachs were analysed to quantify the contribution of zooplankton in their diets, which revealed a dominance of Tropodiaptomus females and the electivity indices proved that T. simplex females (with or without eggs) were highly selected by S. tanganicae, which could probably be explained by size-selective feeding. Life table analysis indicated that approximately 60% of T. simplex nauplii did not develop into copepodites, a loss which could not be explained by the results of the present study. 68% of the fish gut contents were contributed by female Tropodiaptomus individuals and the contribution of shrimps and Cyclopidae increased substantially to almost 20%. S. tanganicae consumed largely ovigerous Tropodiaptomus females. However, eggs found in the guts were significantly smaller than those found in the zooplankton discrete samples, suggesting that digestion had started. The calculated electivity indices underline that ovigerous and non ovigerous females of T. simplex are being positively selected in the feeding process. It infers existence of selective predation in L. Tanganyika by S. tanganicae on females of T. simplex (with or without eggs) and as a result distinct vertical migration as a predation escape mechanism is performed.
Feeding ecology of the intensively fished Nile Perch, Lates niloticus, in Lake Victoria, Uganda
Authors: Nkalubo Winnie , Chapman Lauren , Muyodi Fredrick 
Published: October 2017

The diet of Nile Perch (8.0–121.0 cm total length [TL]) from the Ugandan waters of Lake Victoria was quantified through stomach content analysis of specimens collected from experimental catches and fish factory samples. A total of 7824 stomachs (5602 from experimental fishing and 2222 from factory samples) were examined, of which 34.8% contained food. Fish from the experimental catches were smaller (8.0–41.6 cm TL) and had a higher diversity of prey dominated by unidentifiable fish prey, haplochromine cichlids, Rastrineobola argentea, Odonata and Caridina nilotica, while larger fish (30.0–121.0 cm TL) from the factory samples had a predominance of fish remains and haplochromine cichlids. Nile Perch that had a high proportion of fish prey (versus invertebrates) in their stomachs showed a larger size for a given age, and were in a better condition (K = 1.24) than those that had primarily invertebrates (K = 1.10) in their stomachs. Nile Perch exhibited a much smaller size (15 cm versus 30 cm TL) at shift to piscivory in comparison to Nile Perch examined in earlier studies, when haplochromines were rare in Lake Victoria. The recovery of haplochromine cichlids coincident with declining Nile Perch densities illustrates the importance of developing sustainable management options that can define a proper balance between fishing mortality and Nile Perch predation.
Lake Tanganyika fisheries frame survey analysis: Assessment of the options for management of the fisheries of Lake Tanganyika
Authors: Van der Knaap M. , Katonda K. I. , De Graaf G. J. 
Published: October 2017

From 1999 to 2011 some regions in the Lake Tanganyika Basin experienced humanitarian crises that displaced hundreds of thousands of people to neighboring countries. When relative calm returned to the region in 2008, an influx of displaced peoples and refugees returned to the lake seeking their ancestral fishing grounds. Well-meaning non-governmental organizations and United Nations-organizations donated fishing equipment to these returning people to aid their livelihood opportunities. These fishing programs, however, increased uncontrolled fishing effort on Lake Tanganyika beyond that of previous levels, resulting in decreasing fish catches. Increased monitoring of the fishery, therefore, became essential.In 2009, as a result of uncontrolled fishing effort due to the influx of returnees, inefficient national efforts to monitor their fisheries, and the observed decline of fishery resources, the four countries bordering Lake Tanganyika (Burundi, Democratic Republic of Congo, Tanzania and Zambia) established a regional coordinating body called the Lake Tanganyika Authority to implement fisheries conservation and management measures in compliance with the Convention on the Sustainable Management of Lake Tanganyika. To inform and enable a fisheries monitoring program on Lake Tanganyika, the Authority conducted a lake-wide fisheries frame survey in 2011 to inventory the number of fishermen, fishing units and fisheries infrastructure around Lake Tanganyika.When comparing the 2011 frame survey with data from a similar survey conducted in 1995 (the two most extensive studies to date on Lake Tanganyika), results revealed troubling trends in fish capacity, including: an increase in illegal fishing gear, a doubling of the total number of fishermen and fishing units, and a decline in catch rates since 2002 (based on Burundi data which has been consistently collected).This article analyzes the trends of the Lake Tanganyika fishery, including: fishing effort, the changing uses of gear, and trends in employment in the fishery. Because of the observed increase of fishing capacity (e.g. the numbers of vessels, licenses and fishermen), this article addresses whether an effective fishery management program can be implemented on the lake. Past management efforts have been made from within the basin by the individual countries (Burundi, Democratic Republic of Congo, Tanzania and Zambia), transnational organizations (Food and Agriculture Organization), and the Lake Tanganyika Authority. Using current notions of fishery management on large lakes in the region and ideas from a case study from Gambia, West Africa, this study suggests that effective fishery management on Lake Tanganyika requires the adoption of a formal Monitoring, Control & Surveillance system, community surveillance, an improvement in licensing systems, and a limitation in the number of fishermen and fishing units.
Seasonal and spatial variations of macrobenthic community structure and diversity in the South Yellow Sea
Authors: Xu Yong , Li Xinzheng , Wang Hongfa , Zhang Baolin 
Published: October 2017

Seasonal and spatial characteristics of the macrobenthic community in the South Yellow Sea were studied based on data from three voyages carried out in spring, summer and autumn, 2012. Twenty six stations were sampled and divided into three regions (west, middle and east region of South Yellow Sea). A total of 218 species were obtained with Polychaeta and Crustacea being the predominant groups. Mean abundance varied from 151.4 ind. m−2 in spring to 188 ind. m−2 in autumn showing an increasing trend with season, and mean biomass ranged from 12.1 g m−2 in spring to 33.4 g m−2 in summer. Mean secondary productivity varied from 0.21 g (AFDW)/(m2·month) in spring to 0.48 g (AFDW)/(m2·month) in summer. Biomass was significantly different among seasons, and number of species, secondary productivity and Shannon-Weiner index had significant differences among regions. Abundance, Pielou's evenness index and average taxonomic distinctness were not significantly different among seasons nor regions. Overall significant differences of community structure among both seasons and regions were detected. Depth and the distance from shore were important factors influencing the distribution of macrobenthos in South Yellow Sea.
Improvements in fish polychlorinated biphenyl and other contaminant levels in response to remedial actions in Hamilton Harbour, Ontario, Canada
Authors: Neff Margaret R. , Stefanoff Samantha , Bhavsar Satyendra P. 
Published: October 2017

Hamilton Harbour, located in Ontario, Canada at the western end of Lake Ontario, is recognized as one of the most anthropogenically-impacted regions within the Great Lakes and is currently listed as an Area of Concern. One of the Beneficial Use Impairments for the harbour has been restrictions on fish consumption due to elevated contaminant levels. In this study, we examined past and recent fish contaminant data collected by the Ontario Ministry of the Environment and Climate Change in partnership with other agencies to evaluate temporal trends in fish contaminant concentrations. Measurements for both resident and migratory sport fish as well as juvenile/forage fish were considered, with analysis focused on polychlorinated biphenyls, the group of chemicals identified as the major contaminant of concern. Current contaminant levels were evaluated against fish consumption advisory benchmarks used by Ontario Ministry of the Environment and Climate Change, and compared with corresponding observations for other locations across the Great Lakes, including other Areas of Concern. The results show statistically significant improvements in fish contaminant levels within Hamilton Harbour, with recent fish mercury concentrations below the first advisory benchmarks for all species included in this study. Polychlorinated biphenyl concentrations declined by 59–82% from historical levels, although this decline was not statistically significant in Brown Trout, Common Carp, Freshwater Drum and White Sucker. Further, all species exhibit recent polychlorinated biphenyl concentrations above the first consumption advisory benchmark of 105 ng g−1. Compared to other Great Lakes locations, including other areas of concern, Hamilton Harbour polychlorinated biphenyl concentrations remain amongst the highest. The results suggest that recovery of Hamilton Harbour is still on-going.
Effect of river connectivity on hydrochemistry, sediment enzyme activity and biotic communities of wetlands
Authors: Aftabuddin Md. , Hassan M. A. , Das A. K. , Jha B. C. , Sharma A. P. 
Published: October 2017

Wetlands associated with floodplains of the Ganges and Brahmaputra river systems cover an estimated 0.2 million ha and play a vital role in the fisheries, rural economy and environment. In recent years, most wetlands in the states of Bihar, Assam and West Bengal in India have lost connectivity with their parent rivers due to natural and anthropogenic changes. These changes are causing rapid shrinkage of valuable wetlands and threatening their biodiversity and ecological function. The present study was conducted to assess the effect of river connectivity on the hydrochemistry, sediment enzyme activity, and biotic communities of these wetlands. One wetland area having link channels (open) connecting the main river, and another without link channels (closed), were selected from each of the Ganges and Brahmaputra basins for the study. Comparative analysis of open and closed, ecologically distinct wetlands of the Ganges basin revealed greater seasonal reduction in water depth and higher water conductivity (p &lt; 0.04), nutrients (Ca+2, Mg+2, SiO3-Si), sediment microbial activity (p &lt; 0.004), phosphorous cycling enzymes (p &lt; 0.001), carbon cycling enzymes (p &lt; 0.01), organic matter, conductivity, and plankton and macrozoobenthos (p &lt; 0.01) density in the closed wetland. However, the open wetland showed higher diversity of plankton and macrozoobenthos. A profound impact of connectivity on wetland fisheries was observed in the Brahmaputra basin in Assam, where a higher percentage of catch comprised of indigenous fish species with lower fish yield was noted in the open wetland.
Characterization of polynomials whose large powers have all positive coefficients
Authors: Tan Colin , To Wing-Keung 
Published: October 2017

We give a criterion which characterizes a homogeneous real multi-variate polynomial to have the property that all sufficiently large powers of the polynomial (as well as their products with any given positive homogeneous polynomial) have all positive coefficients. Our result generalizes a result of De Angelis, which corresponds to the case of homogeneous bivariate polynomials, as well as a classical result of Pólya, which corresponds to the case of a specific linear polynomial. As an application, we also give a characterization of certain polynomial spectral radius functions of the defining matrix functions of Markov chains.
On some polynomials and series of Bloch–Pólya type
Authors: Berkovich Alexander , Uncu Ali 
Published: October 2017

We will show that

(
1
−
q
)
(
1
−

q
2

)
…
(
1
−

q
m

)

(1-q)(1-q^2)\dots (1-q^m)

is a polynomial in

q
q

with coefficients from

{
−
1
,
0
,
1
}

\{-1,0,1\}

iff

m
=
1
,

2
,

3
,

m=1,\ 2,\ 3,

or 5 and explore some interesting consequences of this result. We find explicit formulas for the

q
q

-series coefficients of

(
1
−

q
2

)
(
1
−

q
3

)
(
1
−

q
4

)
(
1
−

q
5

)
…

(1-q^2)(1-q^3)(1-q^4)(1-q^5)\dots

and

(
1
−

q
3

)
(
1
−

q
4

)
(
1
−

q
5

)
(
1
−

q
6

)
…

(1-q^3)(1-q^4)(1-q^5)(1-q^6)\dots

. In doing so, we extend certain observations made by Sudler in 1964. We also discuss the classification of the products

(
1
−
q
)
(
1
−

q
2

)
…
(
1
−

q
m

)

(1-q)(1-q^2)\dots (1-q^m)

and some related series with respect to their absolute largest coefficients.
Bartender: a fast and accurate clustering algorithm to count barcode reads
Authors: Zhao Lu , Liu Zhimin , Levy Sasha F , Wu Song 
Published: October 2017

Abstract

Motivation
Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to assay large numbers of cell lineages or genotypes in complex cell pools. Because of its advantages, applications for bar-seq are quickly growing—from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo-barcodes, such as shRNAs or sgRNAs to simultaneously screen large numbers of cell perturbations. However, the computational pipelines for bar-seq clustering are not well developed. Available methods often yield a high frequency of under-clustering artifacts that result in spurious barcodes, or over-clustering artifacts that group distinct barcodes together. Here, we developed Bartender, an accurate clustering algorithm to detect barcodes and their abundances from raw next-generation sequencing data.

Results
In contrast with existing methods that cluster based on sequence similarity alone, Bartender uses a modified two-sample proportion test that also considers cluster size. This modification results in higher accuracy and lower rates of under- and over-clustering artifacts. Additionally, Bartender includes unique molecular identifier handling and a ‘multiple time point’ mode that matches barcode clusters between different clustering runs for seamless handling of time course data. Bartender is a set of simple-to-use command line tools that can be performed on a laptop at comparable run times to existing methods.

Availability and implementation
Bartender is available at no charge for non-commercial use at https://github.com/LaoZZZZZ/bartender-1.1.

Supplementary information
Supplementary data are available at Bioinformatics online.
heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Authors: Galili Tal , O’Callaghan Alan , Sidi Jonathan , Sievert Carson 
Published: October 2017

Abstract

Summary
heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to zoom in to specific sections of the figure from the data matrix, the side dendrograms, or annotated labels. Thanks to the synergistic relationship between heatmaply and other R packages, the user is empowered by a refined control over the statistical and visual aspects of the heatmap layout.

Availability and implementation
The heatmaply package is available under the GPL-2 Open Source license. It comes with a detailed vignette, and is freely available from: http://cran.r-project.org/package=heatmaply.

Supplementary information
Supplementary data are available at Bioinformatics online.
Static output feedback canonical forms
Authors: Yannakoudakis Aristotle G 
Published: October 2017

Abstract
We construct complete static output feedback (SOF) invariants and canonical forms of the set of strictly proper full rank, rational, transfer function matrices. We consider the induced action of the SOF group on the set of Plücker coordinates. Some of them are SOF-invariant and that some others vary linearly with the entries of the feedback gain. Further SOF-invariants are constructed based on the consistency conditions of linear systems of equations. The pair of the above two lists of invariants is complete. The proof is given, introducing a new type of factorization. We construct a SOF-canonical form. We apply the results to the class of systems with two inputs two outputs, characterizing the SOF-equivalence classes in the case of four states as to the property of SOF-pole assignability and calculating the constrained dynamics in the case of more than four states.
Recruiting American Indian/Alaska Native Students to Medical School: A Multi-Institutional Alliance in the U.S. Southwest
Authors: Ballejos Marlene P. , Olsen Polly , Price-Johnson Tanisha , Garcia Cindy , Parker Tassy , Sapién Robert E. , Romero-Leggott Valerie 
Published: October 2017

Problem
Despite national efforts to diversify the physician workforce, American Indian/Alaska Native (AI/AN) individuals have the least representation of all major racial and ethnic groups. Limited resources at state medical schools present institution-level recruitment challenges. Unified efforts to engage AI/AN students in premedical education activities are needed.

Approach
The medical schools at the Universities of Arizona (Phoenix and Tucson), Colorado, New Mexico, and Utah identified a collective need to increase student diversity, particularly with regard to AI/AN students. The schools partnered with the Association of American Indian Physicians to support AI/AN students applying to medical school and to grow the overall AI/AN applicant pool. Each year from 2011 to 2016, these institutions hosted a two-day preadmissions workshop (PAW) to prepare participants for applying to medical school.

Outcomes
From 2011 to 2016, 130 AI/AN students participated in the PAWs. Of these, 113 were first-time attendees, 15 participated on two separate occasions, and 1 participated on three separate occasions. Nineteen (21%) of the 90 first-time participants from 2011 to 2015 matriculated to a U.S. medical school in the past five years. Twenty-two of 23 participants (96% response rate) in 2016 responded to the postworkshop survey. Results indicated that interview preparation, individual consultation, and writing preparation ranked as the three most beneficial sessions/activities.

Next Steps
Standardized evaluation of future PAWs will identify best practices for recruiting AI/AN students to medical school, and future initiatives will include more robust measures of success.
Listening to Relaxing Music Improves Physiological Responses in Premature Infants
Authors: Caparros-Gonzalez Rafael A. , de la Torre-Luque Alejandro , Diaz-Piedra Carolina , Vico Francisco J. , Buela-Casal Gualberto 
Published: October 2017

Background:
Premature infants are exposed to high levels of noise in the neonatal intensive care unit (NICU).

Purpose:
This study evaluated the effect of a relaxing music therapy intervention composed by artificial intelligence on respiratory rate, systolic and diastolic blood pressure, and heart rate.

Methods:
A double-blind, randomized, controlled trial was conducted in the NICUs of 2 general public hospitals in Andalusia, Spain. Participants were 17 healthy premature infants, randomly allocated to the intervention group or the control group (silence) at a 1:1 ratio. To be included in the study, the subjects were to be 32 to 36 weeks of gestation at birth (M= 32.33; SD = 1.79) and passed a hearing screening test satisfactorily. The intervention lasted 20 minutes, 3 times a day for 3 consecutive days, while infants were in the incubator. Infants' heart rate, respiratory rate, and blood pressure were assessed before and after each intervention session.

Results:
After each session, the respiratory rate decreased in the experimental group (main between-groups effect (F
1,13 = 6.73, P = .022, η2
partial = 0.34). Across the sessions, the heart rate increased in the control group (main between-groups effect, F
1,11 = 5.09, P = .045, η2
partial = 0.32).

Implications for Research:
Future studies can use this music intervention to assess its potential effects in premature infants.

Implications for Practice:
Nurses can apply the relaxing music intervention presented in this study to ameliorate the impact of the stressful environment on premature infants.
Recall Bias in Low Back Pain Among Workers
Authors: Rasmussen Charlotte Diana Nørregaard , Holtermann Andreas , Jørgensen Marie Birk 
Published: October 2017

Study Design.
A prospective cohort study.

Objective.
The aim of the present study was first to compare monthly measurements of low back pain (LBP) with quarterly and yearly retrospective measurements of LBP, and second to investigate possible bias effects for recall bias of LBP.

Summary of Background Data.
LBP is a subjective experience often measured by a single rating of recalled pain over a certain time interval. However, retrospectively reported pain may be subject to recall bias.

Methods.
The agreement between monthly measurements of LBP and quarterly and yearly retrospective measurements of LBP was evaluated by Spearman rank order correlation coefficients, intraclass correlation coefficients, and Bland-Altman plots. Bias effects for recall bias were investigated by a linear regression model.

Results.
There were no statistical significant differences in mean values of monthly measurements of LBP compared with quarterly and yearly retrospective measurements of LBP on a group level. However, the Bland-Altman plots revealed that within individuals, the difference between monthly measurements of LBP and quarterly and yearly retrospective measurements of LBP was highly variable. For both quarterly and yearly recall, social support from colleagues and average LBP days were significantly associated with the recall bias.

Conclusion.
The agreement of pain recall among workers in the current study seems to be good on a group level, but both between and within individuals, the difference between monthly and quarterly and yearly retrospective measurements was quite high. Factors that impacted the recall bias were social support from colleagues and average LBP days over the recall period.

Level of Evidence: 3