bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-diagnostic loss to follow-up in an active case-finding TB program: a mixed-methods study from rural Bihar, India
Authors: Garg Tushar , Gupta Vivek , Sen Dyuti , Verma Madhur , Brouwer Miranda , Mishra Rajeshwar , Bhardwaj Manish 
Published: August 2019

ABSTRACTbackgroundDespite active case-finding (ACF) identifying more presumptive and confirmed TB cases, high pre-diagnostic loss to follow-up (PDLFU) among presumptive TB cases referred for diagnostic test remains a concern. We aimed to quantify the PDLFU, and identify the barriers and enablers in undergoing a diagnostic evaluation in an ACF program implemented in 1.02 million rural population in the Samastipur district of Bihar, India.methodsDuring their routine work, Accredited Social Health Activists (ASHA, a community health worker or CHW), informal providers, and community laypersons identified people at risk of TB, and referred them to the program. A field coordinator (FC) screened them for TB symptoms at the patient’s home. The identified presumptive TB cases were accompanied by the CHW to a designated government facility for diagnostics. Those with a confirmed TB diagnosis were put on treatment by the CHW and followed-up till treatment completion. All services were provided free of cost and patients were supported throughout the care pathway, including a transport allowance. We analyzed programmatically collected data, conducted in-depth interviews with patients, and focus group discussions with the CHWs and FCs in an explanatory mixed-methods design.resultsA total of 11146 presumptive TB cases were identified from January 2018 to December 2018, out of which 4912 (44.1%) underwent a diagnostic evaluation. The key enablers were CHW accompaniment and support in addition to the free TB services in the public sector. The major barriers identified were transport challenges, deficient family and health provider support, and poor services in the public system.conclusionIf we are to find missing cases, the health system needs urgent reform, and diagnostic services need to be patient-centric. A strong patient support system engaging all stakeholders and involvement of CHWs in routine TB care is an effective solution.STRENGTHS AND LIMITATIONS OF THIS STUDYFirst such study to explore the reasons for pre-diagnostic loss to follow-upA mixed-method design including the views of both patients and community health workersUses operational data from a routine programmatic setting at an NGO siteNo record of the actual number of people screened intuitively before being referred to the program.No record of patients accessing diagnostics in private sector and those completing the diagnostic process.
Easy MPE: Extraction of quality microplot images for UAV-based high-throughput field phenotyping
Authors: Tresch Léa , Mu Yue , Itoh Atsushi , Kaga Akito , Taguchi Kazunori , Hirafuji Masayuki , Ninomiya Seishi , Guo Wei 
Published: August 2019

AbstractMicroplot extraction (MPE) is a necessary image-processing step in unmanned aerial vehicle (UAV)-based research on breeding fields. At present, it is manually using ArcGIS, QGIS or other GIS-based software, but achieving the desired accuracy is time-consuming. We therefore developed an intuitive, easy-to-use semi-automatic program for MPE called Easy MPE to enable researchers and others to access reliable plot data UAV images of whole fields under variable field conditions. The program uses four major steps: (1). Binary segmentation, (2). Microplot extraction, (3). Production of *.shp files to enable further file manipulation, and (4). Projection of individual microplots generated from the orthomosaic back onto the raw aerial UAV images to preserve the image quality. Crop rows were successfully identified in all trial fields. The performance of proposed method was evaluated by calculating the intersection-over-union (IOU) ratio between microplots determined manually and by Easy MPE: The average IOU (±SD) of all trials was 91% (±3).
The Five-Primer Challenge: An inquiry-based laboratory module for synthetic biology
Authors: Hsu Suzie , Huenemann Jay , Kulkarni Vishwesh , Ledesma-Amaro Rodrigo , Moseley Robert , Mukhitov Nikita , Tiwari Rashmi , Wang Shue , Smanski Michael J. 
Published: August 2019

AbstractNew technologies in DNA synthesis and assembly give genetic engineers complete freedom in genetic design, where virtually any plasmid DNA sequence can be created efficiently and economically. Learning how to design, construct, and test new DNA sequences is a critical skill for researchers in molecular biology and biotechnology. Here we present a student-centered, inquiry-based module in which students learn how to control bacterial gene expression by appplying various DNA assembly techniques. The central activity in this learning module is termed the ‘Five-Primer Challenge’. Each student is allowed to order up to five 60-mer oligonucleotide primers to then modify a GFP expression plasmid with the goal of increasing GFP expression as much as possible. This module was developed and implemented at the 2016 Cold Spring Harbor Laboratory Synthetic Biology Course, and was effective at engaging students in critical thinking and in promoting student learning.
A New Technique and Device for Controlled and Continuous Drug Delivery into the Brain – A Proof of Concept Study
Authors: Anoop U.R. , Verma Kavita 
Published: August 2019

AbstractBackgroundDrug delivery into the brain has been a challenge for the past 100 years because of the blood brain barrier. The existing non-invasive techniques cannot provide controlled and continuous drug delivery into the brain and the invasive techniques make the brain prone to infection from external agents. Hence a new technique which can provide controlled and continuous drug delivery without the need for any surgical intervention in the brain holds immense potential.ObjectiveThe objective of this study is to deliver drugs into the brain using a novel oral and maxillofacial technique and device.MethodDrug delivery into the brain from the oral and maxillofacial region was tested using a novel technique and device in an in vivo rabbit model and an ex vivo goat head model. A control animal and an experimental animal were used in each study. Drugs which do not cross the blood brain barrier normally were tested. Dopamine was delivered in vivo from the maxillo-facial region. Anti-glial fibrillary acidic protein antibody was delivered ex vivo from the oral region. Samples were collected from different sites including the brain and the optic nerve.ResultsThe in vivo model showed a significant increase of dopamine at the pons (51.89%), midbrain (27%), medulla (48.5%) and cortex (72.637%). On including samples from other regions in the t-test, the increase was not statistically significant (p=0.538), suggestive of a central feedback mechanism for brain and peripheral dopamine. A decrease in plasma dopamine during drug delivery further supported a central control for dopamine. In the ex vivo model, a statistically significant (p=0.047) delivery of antibodies occurred at multiple sites including pons (86.7%), cortex (256.5%), and the optic nerve (128.8%).ConclusionThis technique and device can deliver drugs into the brain without detectable increase in systemic circulation. Therefore it may be used for delivering drugs in Parkinson’s disease, Alzheimer’s disease, Pain management, Brain tumors especially pontine tumors, infections like neuro-AIDS, Basal meningitis etc. Retinal drug delivery may also be possible.
Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA
Authors: Peddu Vikas , Bradley Benjamin T. , Shree R. Swati , Colbert Brice G. , Xie Hong , Santo Tracy K. , Huang Meei-Li , Cheng Edith Y. , Konnick Eric , Salipante Stephen J. , Jerome Keith R. , Lockwood Christina M. , Greninger Alexander L. 
Published: August 2019

AbstractCongenital human cytomegalovirus (CMV) infections are the leading cause of newborn hearing and central nervous system impairments worldwide. Currently, routine prenatal screening for congenital CMV is not performed in the United States and confirmation in suspected perinatal cases requires invasive sampling by amniocentesis. We hypothesized that detection of CMV from maternal cell-free DNA (cfDNA) plasma could provide a non-invasive indicator of congenital CMV infection. We analyzed sequence data from 2,208 individuals undergoing routine non-invasive prenatal aneuploidy screening at the University of Washington. CMV reads were identified in 117 (5.3%) samples. Positive samples were stratified based on CMV reads per million sample reads (RPM), resulting in ten samples being classified as strong positive (RPM > 0.3) and 107 as intermediate positive (0.01<RPM<0.3). Subsequent qPCR testing identified CMV in 9/10 strong positive samples and 2/32 intermediate positive samples. Median cfDNA insert size derived from CMV was significantly shorter than cfDNA derived from human chromosomes (103 vs 172 bp, p<0.0001), corresponding to the 3rdpercentile of human cfDNA insert size. In addition, CMV cfDNA fragment lengths were distributed over a wider range than human cfDNA reads. These studies reveal the highly fragmented nature of CMV cfDNA and offer precise measurements of its length: these features likely explain discrepancies in serum CMV viral loads measurements determined by different qPCR assays, despite widespread efforts to standardize results. More work is required to determine how detection of CMV from maternal cfDNA can be best used as tool for congenital CMV screening or diagnosis.
Arginine valency inC9ORF72dipolypeptides mediates promiscuous proteome binding that stalls ribosomes, disable actin cytoskeleton assembly and impairs arginine methylation of endogenous proteins
Authors: Radwan Mona , Ang Ching-Seng , Ormsby Angelique R. , Cox Dezerae , Daly James C. , Reid Gavin E. , Hatters Danny M. 
Published: August 2019

ABSTRACTC9ORF72-associated Motor Neuron Disease patients feature abnormal expression of 5 dipeptide repeat (DPR) polymers. Here we used quantitative proteomics in a Neuro2a cell model to demonstrate that the valency of Arg in the most toxic DPRS, PR and GR, drives promiscuous binding to the proteome, compared to a relative sparse binding of the more inert AP and GA. Notable targets included ribosomal proteins, translation initiation factors and translation elongation factors. PR and GR comprising more than 10 repeats robustly stalled the ribosome suggesting high-valency Arg electrostatically jams the ribosome exit tunnel during synthesis. Poly-GR also bound to arginine methylases and induced hypomethylation of endogenous proteins, with a profound destabilization of the actin cytoskeleton. Our findings point to arginine in GR and PR polymers as multivalent toxins to translation as well as arginine methylation with concomitant downstream effects on widespread biological processes including ribosome biogenesis, mRNA splicing and cytoskeleton assembly.SIGNIFICANCE STATEMENTThe major genetic cause of MND are mutations in an intron of theC9ORF72gene that lead to the expansion in the length of a hexanucleotide repeat sequence, and subsequent non-AUG mediated translation of the intron into 5 different DPRs. The two DPRs containing Arg are potently toxic in animal and cell models. Our research shows that the valency of Arg mediates widespread proteome binding especially affecting machinery involved in Arg-methylation, cytoskeleton and translation. We suggest the mechanisms for toxicity are multipronged and involve electrostatic jamming of ribosomes during translation, acting as substrate mimetics for arginine methylase activity that renders the endogenous proteome hypomethylated and impairing actin cytoskeleton assembly. These mechanisms explain pathologic signatures previous reported in human brain pathology.
Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity
Authors: Grinshpon Robert D. , Shrestha Suman , Titus-McQuillan James , Hamilton Paul T. , Swartz Paul D. , Clark A. Clay 
Published: August 2019

AbstractApoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases require an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared to caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
Visual looming and receding networks in awake marmosets investigated with fMRI
Authors: Cléry Justine C. , Schaeffer David J. , Hori Yuki , Gilbert Kyle M. , Hayrynen Lauren K. , Gati Joseph S. , Menon Ravi S. , Everling Stefan 
Published: August 2019

AbstractAn object that is looming toward a subject or receding away contains important information for determining if this object is dangerous, beneficial or harmless to them. This information (motion, direction, identity, time-to-collision, size, velocity) is analyzed by the brain in order to execute the appropriate behavioral responses depending on the context: fleeing, freezing, grasping, eating, exploring. In the current study, we performed ultra-high-field functional MRI (fMRI) in awake marmosets to explore the patterns of brain activation elicited by visual stimuli looming toward or receding away from the monkey. We found that looming and receding visual stimuli both activate a large cortical network in frontal, parietal, temporal and occipital cortex in areas involved in the analysis of motion, shape, identity and features of the objects. Looming stimuli strongly activated a network composed of the pulvinar, superior colliculus, prefrontal cortex and temporal cortical areas. This may underlie the existence of an alert network that processes the visual stimuli looming toward their peripersonal space by extracting the crucial information brought by the stimulus and evaluating its potential consequences to the observer. We hypothesize that this network is involved in the planning of protective behaviors (e.g. fleeing or freezing) and in emotional reaction (e.g. anxiety, fear). These findings support the view that this network is preserved through evolution and that the marmoset is a viable model to study visual and multisensory processes by using fMRI to guide further invasive recordings and/or pharmacological manipulations.Significant statementAn object that is looming toward a subject or receding away contains important information for determining if this object is dangerous, beneficial or harmless to them. Here, we identified the functional network in non-human primates that was activated by visual stimuli looming toward or away from the animals using ultra-high-field functional magnetic resonance imaging. Our findings show that large cortical activations are elicited by both looming and receding visual conditions. However, some activations were specific to the looming condition, suggesting that the integration of cues in the looming direction rely on strong connections between cortical and subcortical areas, which allows primates to react properly for protecting themselves against a potential threat.
Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC
Authors: Reimegård Johan , Danielsson Marcus , Tarbier Marcel , Schuster Jens , Baskaran Sathishkumar , Panagiotou Styliani , Dahl Niklas , Friedländer Marc R. , Gallant Caroline J. 
Published: August 2019

ABSTRACTCombined measurements of mRNA and protein expression in single cells enables in-depth analysis of cellular states. We present single-cell protein and RNA co-profiling (SPARC), an approach to simultaneously measure global mRNA and large sets of intracellular protein in individual cells. Using SPARC, we show that mRNA expression fails to accurately reflect protein abundance at the time of measurement in human embryonic stem cells, although the direction of changes of mRNA and protein expression are in agreement during cellular differentiation. Moreover, protein levels of transcription factors better predict their downstream effects than do the corresponding transcripts. We further show that changes of the balance between protein and mRNA expression levels can be applied to infer expression kinetic trajectories, revealing future states of individual cells. Finally, we highlight that mRNA expression may be more varied among cells than levels of the corresponding proteins. Overall, our results demonstrate that mRNA and protein measurements in single cells provide different and complementary information regarding cell states. Accordingly, SPARC can offer valuable insights in gene expression programs of single cells.
NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells
Authors: Yang Linfeng , Ghosh Rajarshi. P. , Franklin J. Matthew , You Chenyu , Liphardt Jan T. 
Published: August 2019

AbstractSegmenting cell nuclei within microscopy images is a ubiquitous task in biological research and clinical applications. Unfortunately, segmenting low-contrast overlapping objects that may be tightly packed is a major bottleneck in standard deep learning-based models. We report a Nuclear Segmentation Tool (NuSeT) based on deep learning that accurately segments nuclei across multiple types of fluorescence imaging data. Using a hybrid network consisting of U-Net and Region Proposal Networks (RPN), followed by a watershed step, we have achieved superior performance in detecting and delineating nuclear boundaries in 2D and 3D images of varying complexities. By using foreground normalization and additional training on synthetic images containing non-cellular artifacts, NuSeT improves nuclear detection and reduces false positives. NuSeT addresses common challenges in nuclear segmentation such as variability in nuclear signal and shape, limited training sample size, and sample preparation artifacts. Compared to other segmentation models, NuSeT consistently fares better in generating accurate segmentation masks and assigning boundaries for touching nuclei.
An analysis on building elements of a wooden structured granary
Authors: Yazıcıoğlu Fatih , Alkan Seda Nur 
Published: August 2019

PurposeThe purpose of this paper is to make a comprehensive research on serenders including observation, determination and documentation of the architectural details of serender. Moreover, computer simulation-based performance evaluation is also planned to be applied in order to make a contribution to architectural, social, cultural and historical sustainability of serender.Design/methodology/approachThe study employs strategies based on qualitative research techniques and methods. In order to clarify the architectural details of serender structures, literature review and a case study analysis are conducted.FindingsWithin the scope of this paper, the early findings of this ongoing research, which are about the architectural details, are presented regarding the regional characteristics as borders. This part of the study presents the determination of all the original architectural details of serender.Originality/valueSerenders in Rize, Turkey, have original, architectural, cultural and historical values. However, they have not been preferred to be built and used in recent years. Therefore, the original architectural style, details and construction techniques have started to fade away. These facts highlight the importance of their documentation and preservation in terms of traditional architecture, material and craftsmanship. This study aims to provide comprehensive documents about their architectural characteristics.
Communication performance challenges in PPP projects: cases of Ghana and South Africa
Authors: Kwofie Titus Ebenezer , Ohis Aigbavboa Clinton , Thwala Wellington Didibhuku 
Published: August 2019

Purpose
The need to gain theoretical and practical understanding into the communication performance challenges in public private partnership (PPP) projects is considered as a precursor to effective communication strategies, management, planning and improvement in PPP models in both developed and developing countries. Hence, the purpose of this paper is to investigate the nature of communication performance challenges in PPP projects.

Design/methodology/approach
By adopting a deductive research design, a questionnaire survey of participants in the communication network of PPP projects in two countries (Ghana and South Africa) was conducted. The responses were analyzed using mean scores, Kendall’s concordance and Mann–Whitney U test.

Findings
The results revealed communication performance challenges that are unique to PPP project environment. Additionally, there were other typologies of communication challenges such as untimeliness, distortions and protocols that were frequently experienced in Ghana and not in South Africa. Also the emergence of misunderstanding affirmed that indeed this is a communication problem that is common and not peculiar to any project context or country.

Practical implications
With communication challenges and information asymmetries as notable challenges in PPP coupled with suggestions that effective communication is central to success of PPP projects and management, the insight into the communication performance challenges given by this study could be very useful to effective planning and strategies towards communication in construction project delivery in PPP and thus underline the importance of deriving mechanisms and protocols that suit PPP project environments.

Originality/value
These findings can be a precursor for developing bespoke communication systems, tools, protocols and communication behaviours to facilitate information flow aimed at overcoming information asymmetries and ultimately improving the quality of communication actions, tasks and outcomes in PPP project delivery.