bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequences of RIGVIR Oncolytic Virotherapy Virus and Five Other Echovirus 7 Isolates
Authors: Hietanen Eero , Smura Teemu , Hakanen Marika , Chansaenroj Jira , Merilahti Pirjo , Nevalainen Janne , Pandey Sunita , Koskinen Satu , Tripathi Lav , Poovorawan Yong , Pursiheimo Juha , Susi Petri 
Published: April 2018

ABSTRACT
We report here the nearly complete Illumina-sequenced consensus genome sequences of six isolates of echovirus 7 (E7), including oncolytic virotherapy virus RIGVIR and the Wallace prototype. Amino acid identities within the coding region were highly conserved across all isolates, ranging from 95.31% to 99.73%.
Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing
Authors: Tondini Federico , Jiranek Vladimir , Grbin Paul R. , Onetto Cristobal A. 
Published: April 2018

ABSTRACT

Here, we report the first sequenced genome of an indigenous Australian wine isolate of
Torulaspora delbrueckii
using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.
Draft Genome Sequences of the Obligatory Marine Myxobacterial Strains Enhygromyxa salina SWB005 and SWB007
Authors: Amiri Moghaddam Jamshid , Poehlein Anja , Fisch Katja , Alanjary Mohammad , Daniel Rolf , König Gabriele M. , Schäberle Till F. 
Published: April 2018

ABSTRACT

The two marine myxobacterial strains
Enhygromyxa salina
SWB005 and SWB007 were isolated from coastal soil samples using
Escherichia coli
as bait for these predatory strains. These strains produce unique specialized metabolites. Genomes were assembled into 312 contigs for
E. salina
SWB005 (9.0 Mbp) and 192 contigs for
E. salina
SWB007 (10.6 Mbp).
Whole-Genome Sequence of Infectious Pancreatic Necrosis Virus Isolated from Farmed Brook Trout (Salvelinus fontinalis) in Pennsylvania
Authors: Palchak Kay , Chothe Shubhada K. , Sebastian Aswathy , Nissly Ruth H. , Barry Rhiannon , Albert Istvan , Jayarao Bhushan M. , Kuchipudi Suresh V. 
Published: April 2018

ABSTRACT
Infectious pancreatic necrosis (IPN) is an acute contagious systemic disease affecting several fish species and a critical disease in the salmonid fish farming industry. Here, we report the complete genome sequence of IPN virus (IPNV) RNA segments A and B, isolated from a farmed brook trout in Pennsylvania.
Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan
Authors: Ito Toshihiro , Maruyama Fumito , Sawai Kotaro , Nozaki Keiko , Otsu Keiko , Ohya Kenji 
Published: April 2018

ABSTRACT

Mycobacterium virginiense
, a newly described species of the
Mycobacterium terrae
complex, is a cause of tenosynovitis and osteomyelitis in the United States. Here, we report the 4,849,424-bp draft genome sequence of
M. virginiense
strain GF75, isolated from a mud sample taken from a Japanese swine farm.
Quantifying the mechanical and histological properties of thrombus analog made from human blood for the creation of synthetic thrombus for thrombectomy device testing
Authors: Merritt William , Holter Anne Marie , Beahm Sharna , Gonzalez Connor , Becker Timothy A , Tabor Aaron , Ducruet Andrew F , Bonsmann Laura S , Cotter Trevor R , Frenklakh Sergey 
Published: April 2018

BackgroundUntreated ischemic stroke can lead to severe morbidity and death, and as such, there are numerous endovascular blood-clot removal (thrombectomy) devices approved for human use. Human thrombi types are highly variable and are typically classified in qualitative terms – ‘soft/red,’ ‘hard/white,’ or ‘aged/calcified.’ Quantifying human thrombus properties can accelerate the development of thrombus analogs for the study of thrombectomy outcomes, which are often inconsistent among treated patients.Methods‘Soft’human thrombi were created from blood samples ex vivo (ie, human blood clotted in sample vials) and tested for mechanical properties using a hybrid rheometer material testing system. Synthetic thrombus materials were also mechanically tested and compared with the ‘soft’ human blood clots.ResultsMechanical testing quantified the shear modulus and dynamic (elastic) modulus of volunteer human thrombus samples. This data was used to formulate a synthetic blood clot made from a composite polymer hydrogel of polyacrylamide and alginate (PAAM-Alg). The PAAM-Alg interpenetrating network of covalently and ionically cross-linked polymers had tunable elastic and shear moduli properties and shape memory characteristics.ConclusionsDue to its adjustable properties, PAAM-Alg can be modified to mimic various thrombi classifications. Future studies will include obtaining and quantitatively classifying patient thrombectomy samples and altering the PAAM-Alg to mimic the results for use with in vitro thrombectomy studies.
IN-SITU DETECTION OF HEAVY METAL POLLUTION IN SEAWATER WITH DIAMOND COATED ELECTRODES
Authors: ZHAO BIN , LI JIA , YU XIANG , ZHANG JING , REN YI 
Published: April 2018

Heavy metal pollution endangers seawater and there is urgent need for the development of effective detectors that can provide warning of heavy metal pollution. Anodic stripping voltammetry is applicable for the detection of heavy metal pollution in sea water, but it suffers from two problems that are associated with the mercury electrode used: one is insufficient sensitivity and the other is secondary pollution caused by toxic mercury. In this work, we employed boron-doped diamond electrode as an alternative to mercury electrode for the detection of heavy metals. The BDD electrode was fabricated and its electrochemical properties were ascertained. The results of this work showed that: (1) the electrode prepared has a wide electrochemical window (4.2 V) and low background current ([Formula: see text]A). (2) multiple heavy metals (Pb[Formula: see text], Cd[Formula: see text], Zn[Formula: see text] and Cu[Formula: see text]) in seawater samples are detected simultaneously with the optimized electrode, with high sensitivity and good repeatability. (3) the repeatability of the detection meets the values stipulated in the national standard. The detection period is less than 15[Formula: see text]min, and in situ monitoring of heavy metals in seawater can be achieved by automatic sampling and wireless data transmission.
Commenting on code, considering data's bottleneck
Authors: Torres Edwin , Saba Walid 
Published: April 2018

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM
http://cacm.acm.org/blogs/blog-cacm
Edwin Torres considers the enduring value of code comments, while Walid Saba wonders if we have overreacted to the knowledge acquisition bottleneck.
Signals driving the adaptation of saccades that require spatial updating
Authors: Soetedjo Robijanto 
Published: April 2018

Saccades adapt to persistent natural or artificially imposed dysmetrias. The characteristics and circuitry of saccade adaptation have been revealed using a visually guided task (VGT) where the vectors of the target step and the intended saccade command are the same. However, in real life, another saccade occasionally intervenes before the saccade to the target occurs. This necessitates an updating of the intended saccade to account for the intervening saccadic displacement, which dissociates the visual target signal and the intended saccade command. We determined whether the adaptation process is similar for VGT and updated saccades by studying the transfer of adaptation between them. The ultimate visual target was dissociated from the intended saccade command with double-step saccade tasks (DSTs) in which two targets are flashed sequentially at different locations while the monkey maintains fixation. The resulting saccades toward the first and second targets occur in the dark. The transfer of visually guided saccade adaptation to the second saccades of a DST and vice versa depended on the eccentricity of the second visual target, and not the second saccade command. If a target with the same eccentricity as the adapted target appears briefly during the intersaccadic interval of a DST, more adaptation transfers. Because a brief appearance of the visual target either before the first saccade or during the intersaccadic interval influences how much adaptation transfer the second saccade will express, the processing of adaptation and DST updating may overlap. NEW & NOTEWORTHY Adaptation and the spatial updating of saccades are thought to be independent processes. When we dissociate the visual target and the intended saccade command, the transfer of visually guided saccade adaptation to the saccades of the double-step saccade tasks (DST) and vice versa is driven by a visual not motor error. The visual target has an effect until the second saccade of a DST occurs. Therefore, the processing of adaptation and the spatial updating of saccades may overlap.
Stable long-term BCI-enabled communication in ALS and locked-in syndrome using LFP signals
Authors: Milekovic Tomislav , Sarma Anish A. , Bacher Daniel , Simeral John D. , Saab Jad , Pandarinath Chethan , Sorice Brittany L. , Blabe Christine , Oakley Erin M. , Tringale Kathryn R. , Eskandar Emad , Cash Sydney S. , Henderson Jaimie M. , Shenoy Krishna V. , Donoghue John P. , Hochberg Leigh R. 
Published: April 2018

Restoring communication for people with locked-in syndrome remains a challenging clinical problem without a reliable solution. Recent studies have shown that people with paralysis can use brain-computer interfaces (BCIs) based on intracortical spiking activity to efficiently type messages. However, due to neuronal signal instability, most intracortical BCIs have required frequent calibration and continuous assistance of skilled engineers to maintain performance. Here, an individual with locked-in syndrome due to brain stem stroke and an individual with tetraplegia secondary to amyotrophic lateral sclerosis (ALS) used a simple communication BCI based on intracortical local field potentials (LFPs) for 76 and 138 days, respectively, without recalibration and without significant loss of performance. BCI spelling rates of 3.07 and 6.88 correct characters/minute allowed the participants to type messages and write emails. Our results indicate that people with locked-in syndrome could soon use a slow but reliable LFP-based BCI for everyday communication without ongoing intervention from a technician or caregiver. NEW & NOTEWORTHY This study demonstrates, for the first time, stable repeated use of an intracortical brain-computer interface by people with tetraplegia over up to four and a half months. The approach uses local field potentials (LFPs), signals that may be more stable than neuronal action potentials, to decode participants’ commands. Throughout the several months of evaluation, the decoder remained unchanged; thus no technical interventions were required to maintain consistent brain-computer interface operation.
Mechanisms of Acquired Resistance to Trastuzumab Emtansine in Breast Cancer Cells
Authors: Li Guangmin , Guo Jun , Shen Ben-Quan , Yadav Daniela Bumbaca , Sliwkowski Mark X. , Crocker Lisa M. , Lacap Jennifer A. , Phillips Gail D. Lewis 
Published: April 2018

AbstractThe receptor tyrosine kinase HER2 is overexpressed in approximately 20% of breast cancer, and its amplification is associated with reduced survival. Trastuzumab emtansine (Kadcyla, T-DM1), an antibody–drug conjugate that is comprised of trastuzumab covalently linked to the antimitotic agent DM1 through a stable linker, was designed to selectively deliver DM1 to HER2-overexpressing tumor cells. T-DM1 is approved for the treatment of patients with HER2-positive metastatic breast cancer following progression on trastuzumab and a taxane. Despite the improvement in clinical outcome, many patients who initially respond to T-DM1 treatment eventually develop progressive disease. The mechanisms that contribute to T-DM1 resistance are not fully understood. To this end, we developed T-DM1–resistant in vitro models to examine the mechanisms of acquired T-DM1 resistance. We demonstrate that decreased HER2 and upregulation of MDR1 contribute to T-DM1 resistance in KPL-4 T-DM1–resistant cells. In contrast, both loss of SLC46A3 and PTEN deficiency play a role in conferring resistance in BT-474M1 T-DM1–resistant cells. Our data suggest that these two cell lines acquire resistance through distinct mechanisms. Furthermore, we show that the KPL-4 T-DM1 resistance can be overcome by treatment with an inhibitor of MDR1, whereas a PI3K inhibitor can rescue PTEN loss–induced resistance in T-DM1–resistant BT-474M1 cells. Our results provide a rationale for developing therapeutic strategies to enhance T-DM1 clinical efficacy by combining T-DM1 and other inhibitors that target signaling transduction or resistance pathways. Mol Cancer Ther; 17(7); 1441–53. ©2018 AACR.
Selective Targeting and Eradication of LGR5+ Cancer Stem Cells Using RSPO-Conjugated Doxorubicin Liposomes
Authors: Cao Jing , Li Chong , Wei Xiaohui , Tu Meiqing , Zhang Yan , Xu Fengwei , Xu Yuhong 
Published: April 2018

Abstract
Cancer stem cells (CSC) that may account for only a small fraction of tumor mass were found to play crucial roles during tumor initiating, progression, and metastasis. However, they are usually difficult to be treated and notoriously resilient to drug eradication. In this study, we aimed at the Wnt signaling characteristic of CSCs and designed a liposomal drug delivery system to target CSCs. Liposomes decorated with RSPO1 on the surface were constructed for specific interactions with the Wnt pathway coreceptor LGR5. Doxorubicin carried by the RSPO1-liposomes was more effective at lower concentrations than the same drug loaded in PEG-liposomes. More importantly, we showed using a patient-derived xenograft tumor model where LGR5+ CSCs coexisted with LGR5− cells, the RSPO1-liposomes were able to access more CSC cells and deliver the drug specifically and efficiently. Such a focused effect in eradicating LGR5+ cells led to massive tumor tissue necrosis and growth inhibition even when only a fraction of the conventional drug dose was used. These data clearly demonstrated the advantages of CSC-targeted drug delivery and would support the development of such approaches as a new cancer treatment strategy. Mol Cancer Ther; 17(7); 1475–85. ©2018 AACR.
Improving the In Vivo Efficacy of an Anti-Tac (CD25) Immunotoxin by Pseudomonas Exotoxin A Domain II Engineering
Authors: Kaplan Gilad , Mazor Ronit , Lee Fred , Jang Youjin , Leshem Yasmin , Pastan Ira 
Published: April 2018

Abstract
Tac (CD25) is expressed on multiple hematologic malignancies and is a target for cancer therapies. LMB-2 is an extremely active anti-Tac recombinant immunotoxin composed of an Fv that binds to Tac and a 38-kDa fragment of Pseudomonas exotoxin A (PE38). Although LMB-2 has shown high cytotoxicity toward Tac-expressing cancer cells in clinical trials, its efficacy was hampered by the formation of anti-drug antibodies against the immunogenic bacterial toxin and by dose-limiting off-target toxicity. To reduce toxin immunogenicity and nonspecific toxicity, we introduced six point mutations into domain III that were previously shown to reduce T-cell immunogenicity and deleted domain II from the toxin, leaving only the 11aa furin cleavage site, which is required for cytotoxic activity. Although this strategy has been successfully implemented for mesothelin and CD22-targeting immunotoxins, we found that removal of domain II significantly lowered the cytotoxic activity of anti-Tac immunotoxins. To restore cytotoxic activity in the absence of PE domain II, we implemented a combined rational design and screening approach to isolate highly active domain II–deleted toxin variants. The domain II–deleted variant with the highest activity contained an engineered disulfide-bridged furin cleavage site designed to mimic its native conformation within domain II. We found that this approach restored 5-fold of the cytotoxic activity and dramatically improved the MTD. Both of these improvements led to significantly increased antitumor efficacy in vivo. We conclude that the next-generation anti-Tac immunotoxin is an improved candidate for targeting Tac-expressing malignancies. Mol Cancer Ther; 17(7); 1486–93. ©2018 AACR.
Allelic Polymorphisms of KIRs and HLAs Predict Favorable Responses to Tyrosine Kinase Inhibitors in CML
Authors: Ureshino Hiroshi , Shindo Takero , Kojima Hiroto , Kusunoki Yasushi , Miyazaki Yuki , Tanaka Hidenori , Saji Hiroh , Kawaguchi Atsushi , Kimura Shinya 
Published: April 2018

Abstract
Response to tyrosine kinase inhibitors (TKIs) is variable in chronic myeloid leukemia (CML), and elevated natural killer (NK) cells during TKI therapy are positively correlated with superior outcomes. NK cell function involves interactions of their killer immunoglobulin-like receptors (KIRs) and human leukocyte antigen (HLA) class I on target cells, and the avidity of KIR–HLA interactions depends on the combination of KIR and HLA alleles. We hypothesized that KIR and HLA polymorphisms may influence response to TKIs. KIR and HLA allele genotyping was performed by next-generation sequencing for 76 CML cases, and association with clinical outcome was analyzed. Second-generation TKIs as first-line therapy and patients' sex (female) were strongly associated with achievement of complete molecular response (CMR: MR4.0) after 2 years (P &lt; 0.001 and P = 0.002, respectively). After adjustment for these two characteristics, several KIR alleles remained associated with achievement of MR4.0: KIR2DL4*005/011 or *008 (HR = 1.797, P = 0.032); KIR2DS4*003 or *007/010 (HR = 3.348, P &lt; 0.001); KIR3DL1*005 (HR = 2.746, P = 0.003); and KIR3DL2*009 or *010 [HR = 1.980 (1.109–3.524), P = 0.021]. Strong linkage among these alleles exists, implying that they comprise favorable KIR allele haplotypes. Allelic polymorphisms of KIR3DL1 and HLA-B determine their differential avidity into strong/weak or no interaction. Patients carrying noninteracting KIR3DL1 and HLA-B allele pairs achieved better outcomes than those with strongly interacting pairs, and KIR3DL1*005 associated with a positive outcome among patients with weak-interacting pairs. Thus, KIR3DL1*005 and its associated haplotypes associated with superior TKI therapeutic effects. The combinations of these KIR and HLA alleles may correlate with potent NK cell immunity against CML. Cancer Immunol Res; 6(6); 745–54. ©2018 AACR.
ЕКСПЕРИМЕНТАЛЬНЕ ОБҐРУНТУВАННЯ СКЛАДУ НАЗАЛЬНОГО ГЕЛЮ ПІД УМОВНОЮ НАЗВОЮ «ФІТОРИН-ПЛЮС»
Authors: Karpenko I. A. , Yarnykh T. G. , Rukhmakova O. A. 
Published: April 2018

Мета роботи. Експериментальне обґрунтування складу назального гелю під умовною назвою «Фіторин-плюс».Матеріали і методи. З метою визначення раціональної концентрації екстракту кореня солодки та ефірних олій евкаліпту прутоподібного і сосни сибірської у складі гелю були проведені мікробіологічні дослідження на базі кафедри мікробіології, вірусології та імунології Національного фармацевтичного університету в лабораторії мікробіологічних та імунологічних досліджень методом дифузії в агар з використанням еталонних штамів мікроорганізмів: Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Candida albicans ATCC 885/653. Дослідження з вивчення противірусної активності здійснювали на базі Державної установи «Інститут мікробіології та імунології ім. І. І. Мечникова АМН України».Результати й обговорення. На підставі проведених досліджень були обґрунтовані раціональні концентрації діючих речовин у складі назального гелю «Фіторин-плюс»: екстракту кореня солодки – 3 %, ефірної олії евкаліпту прутоподібного – 2 %, ефірної олії сосни сибірської – 1 %. Отримані дані були підтверджені при подальшому експериментальному вивченні антимікробних і противірусних властивостей готової лікарської форми.Висновки. Експериментально обґрунтовано вибір діючих речовин назального гелю під умовною назвою «Фіторин-плюс» для лікування ринітів. На підставі даних проведених мікробіологічних досліджень обґрунтовано концентрацію екстракту кореня солодки й ефірних олій у складі лікарського препарату. Вперше встановлено противірусну дію екстракту кореня солодки відносно аденовірусу. Показано, що розроблений назальний гель є перспективним для подальшого використання в терапії ринітів.
НОВИЙ ПІДХІД ДО ІДЕНТИФІКАЦІЇ ОКСИБУПРОКАЇНУ В ЛІКАРСЬКИХ ЗАСОБАХ
Authors: Levin M. G. , Britsun V. N. , Tarasenko N. L. , Savina N. A. , Оstanina N. V. 
Published: April 2018

Мета роботи. Розробка покращеного безсірковуглецевого методу визначення оксибупрокаїну в лікарських засобах.Матеріали і методи. Ідентифікація активного фармацевтичного інгредієнта оксибупрокаїну в лікарських засобах методом ІЧ-спектроскопії в таблетках KBr після екстракції його летким органічним розчинником.Результати й обговорення. Замість сірковуглецю для екстракції основи оксибупрокаїну використано менш пожежонебезпечний і менш токсичний н-гексан. Після випаровування розчинника реєструвались в одна­кових умовах ІЧ-спектри стандартного зразка та досліджуваної речовини (випробовуваного зразка). Порівняння ІЧ-спектрів показує їх збіг на 95 %, що підтверджує правомірність заміни сірковуглецю на н-гек­сан.Висновок. Розроблений підхід має переваги щодо відомої методики з огляду на відсутність пожежонебезпечного та отруйного сірковуглецю.Ключові слова: оксибупрокаїн; сірковуглець; н-гексан; ІЧ-спектроскопія; ідентифікація.
АНАЛІЗ ПРИЗНАЧЕНЬ СХЕМ АНТИРЕТРОВІРУСНОЇ ТЕРАПІЇ ВІЛ-ІНФІКОВАНИМ ОСОБАМ В УКРАЇНІ
Authors: Fedyak I. O. 
Published: April 2018

Мета роботи. Провести аналіз призначень схем антиретровірусної терапії (АРТ) у реальній практиці людей, які живуть з ВІЛ (ЛЖВ), у 12-ти областях України та порівняти отримані результати з даними національного Звіту про надання АРТ ВІЛ-інфікованим особам.Матеріали і методи. Використано 1 200 карт диспансерного нагляду за ВІЛ-інфікованою особою Ф030-5/о, отриманих із 12-ти обласних СНІД-центрів Вінницької, Дніпропетровської, Запорізької, Івано-Франківської, Львівської, Миколаївської, Одеської, Рівненської, Тернопільської, Харківської, Херсонської областей та м. Києва у липні–листопаді 2016 р. (зі збереженням таємниці особистих даних ЛЖВ); дані Звіту про надання АРТ ВІЛ-інфікованим Центру громадського здоров’я МОЗ України; методи: частотний аналіз, АВС-аналіз призначень.Результати й обговорення. П’ять схем АРТ є основними у призначеннях ЛЖВ в Україні – 1л: TDF+FTC(ЗТС)+EFV (39,0 % за Звітом / 36,4 % у вибірці), 1д: AZT+3TC+LPV/r (15,0 % / 17,5 %), 1а: AZT+3TC+EFV (14,2 % / 13,0 %), 1о: TDF/FTC+LPV/r (8,9 % / 9,0 %), 1п: ABC+3TC+LPV/r (6,2 % / 6,5 %), оскільки їх сумарно приймали 83,26 % / 82,42 % ЛЖВ.Висновки. За результатом власних досліджень, 1 200 ЛЖВ 1 777 раз призначали схеми АРТ. З усіх хворих – 66,17 % залишалися на первинній схемі АРТ першого ряду, а її заміни відбувалися від одного (23,5 %) до п’яти (0,17 %) раз. Схема АРТ, рекомендована ВООЗ, була лідером призначень (36,44 %): TDF+FTC+EFV найчастіше призначали у Запорізькій (57 %), Івано-Франківській (49 %), Рівненській (40 %), Одеській (24 %), Львівській (23 %) областях. На другому місці – схема 1д: AZT+ЗTC+LPV/r (17,5 %), яка була лідером у Херсонській (31 %) та розділила лідерство зі схемою 1л у Миколаївській (24 %) областях.