bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV-1 sequences in lentiviral vector genomes can be substantially reduced without compromising transduction efficiency
Authors: Sertkaya Helin , Ficarelli Mattia , Sweeney Nathan P , Parker Hannah , Vink Conrad A , Swanson Chad M 
Published: February 2021

Abstract
Many lentiviral vector genomes used for gene therapy are derived from HIV-1 and contain sequences required for genome expression, encapsidation and reverse transcription. In addition, they contain substantial regions of gag and env. Extraneous viral sequence in the genome reduces the maximum size of the transgene expression cassette and potentially increases biosafety concerns. Importantly, it remains unclear whether all of the HIV-1 sequence is required for transduction efficiency. To determine the functional relevance of the viral sequences in the vector genome, we performed a deletion analysis. Most of gag could be deleted without compromising vector titre. Within env, only the RRE is necessary, allowing over 50% of this region to be deleted. Oxford Nanopore sequencing showed that deleting 507 nt of env decreased the number of pre-mRNA splicing events per transcript and increased the proportion of unspliced genomes. Finally, combining the deletion in gag with moving the RRE downstream of the 3’ R to prevent its reverse transcription showed that substantial amounts of HIV-1 sequence can be removed from the vector genome without compromising transduction efficiency. Overall, this allows the creation of lentiviral vector genomes that contain minimal HIV-1 sequence, which could improve biosafety and increase the transgene capacity.
Fluid-Screen as a Real Time Dielectrophoretic Method for Universal Microbial Capture
Authors: Weber Monika , Weber Robert , Petkowski Janusz , Michaels Brandye , Wisniewski Kamil , Piela Anna , Antoszczyk Slawomir 
Published: February 2021

Abstract
Dielectrophoresis (DEP) has shown great promise for particle separation for decades; however, it has not yet been widely applied in routine laboratory setting. This paper provides an overview of a new DEP microbial capture and separation method called Fluid-Screen (FS), that achieves an efficient, reliable and repeatable capture and separation of microbial cells. Method verification experiments demonstrated that the FS system captured 100% of bacteria in test samples, a capture efficiency much higher than previously reported for similar technology. Data generated supports the superiority of the FS method as compared to the established Plate Counting Method (PCM), that is routinely used to detect bacterial contamination in healthcare, pharmacological and food industries. We have established that the FS method is universal and can capture and separate different species of bacteria and fungi to viruses, from various sample matrices (i.e. human red blood cells, mammalian cells).
GNG5 is a novel oncogene associated with cell migration, proliferation, and poor prognosis in glioma
Authors: Zhang Wang , Liu Zhendong , Liu Binchao , Jiang Miaomiao , Yan Shi , Han Xian , Shen Hong , Na Meng , Wang Yanbiao , Ren Zhishuai , Liu Binfeng , Gao Yanzheng , Jiang Zhenfeng , Lin Zhiguo 
Published: February 2021

Abstract
Background: Although many biomarkers have been reported for detecting glioma, the prognosis for the disease remains poor, and therefore, new biomarkers need to be identified. GNG5, which is part of the G-protein family, has been associated with different malignant tumors, though the role of GNG5 in glioma has not been studied. Therefore, we aimed to identify the relationship between GNG5 and glioma prognosis and identify a new biomarker for the diagnosis and treatment of gliomas.Methods: We used data on more than a thousand gliomas from multiple databases and clinical data to determine the expression of GNG5 in glioma. Based on clinical data and CGGA database, we identified the correlation between GNG5 and multiple molecular and clinical features and prognosis using various analytical methods. Co-expression analysis and GSEA were performed to detect GNG5-related genes in glioma and possible signaling pathways involved. ESTIMATE, ssGSEA, and TIMER were used to detect the relationship between GNG5 and the immune microenvironment. Functional experiments were performed to explore the function of GNG5 in glioma cells.Results: GNG5 is highly expressed in gliomas, and its expression level is positively correlated with pathological grade, histological type, age, and tumor recurrence and negatively correlated with isocitrate dehydrogenase mutation, 1p/19 co-deletion, and chemotherapy. Moreover, GNG5 as an independent risk factor was negatively correlated with the overall survival time. GSEA revealed the potential signaling pathways involved in GNG5 function in gliomas, including cell adhesion molecules signaling pathway. The ssGSEA, ESTIMATE, and TIMER based analysis indicated a correlation between GNG5 expression and various immune cells in glioma. In vivo and in vitro experiments showed that GNG5 could participate in glioma cell proliferation and migration.Conclusions: Based on the large data platform and the use of different databases to corroborate results obtained using various datasets, as well as in vitro and in vivo experiments, our study reveals for the first time that GNG5, as an oncogene, is overexpressed in gliomas and can inhibit the proliferation and migration of glioma cells and lead to poor prognosis of patients. Thus, GNG5 is a potential novel biomarker for the clinical diagnosis and treatment of gliomas.
A Study of Frequency and Pattern of Adverse Transfusion Reactions at a Blood Bank in a Tertiary Care Hospital: Towards Hemovigilance
Authors: Shajil Suzaan , Adiga Deepa Sowkur Anandarama , Saha Debarshi , Chakraborty Shrijeet , Rao Ranjitha 
Published: February 2021

Background: Adequate and safe transfusion facility of blood and its components is necessary as blood transfusions are a part of life saving measures in medical and surgical emergencies. However, transfusion practice could result in non-fatal to fatal adverse transfusion reactions (ATR). Therefore, it is important to identify various adverse reactions so that steps can be taken to minimize such reactions and ensure safer transfusion being carried out.
Methods: All ATRs reported to the blood bank from January 2013 to December 2016 were reviewed and analysed. The frequency of ATRs and its association with various component types were assessed.
Result: During the study period, a total of 199106 units of blood were issued from the blood bank out of which there was an incidence of 77 (0.12%) transfusion reactions. Chills/rigors was the most common symptom (27.3%) of the symptomatic cases followed by pruritis (23.4%)
Majority of the transfusion reaction were non haemolytic, 76 (98.7%) cases. One case was of haemolytic transfusion reaction. Among the non-haemolytic transfusion reactions, febrile non haemolytic transfusion reaction (FNHTR) constituted 28 (36.4%) and allergic reactions constituted 41(53.2%). Other transfusion reactions including hypotensive transfusion reaction (HTR), 1 (1.3%) case and transfusion associated dyspnoea (TAD), 6 (7.8%) cases were also seen. The frequency of ATRs was highest with packed red cells (PC) being 75.3% and least with platelet concentrate (PLTC) being 11.7%.
Conclusion: The frequency of ATRs in our blood bank was found to be on a lower scale when compared to that of most of the similar studies. Allergic reactions and FNHTR were the most common ATRs seen, introduction of leukoreduction filters would help reduce FNHTRs.
SPECIFIC COMPOSITION OF CHICKPEA PESTS IN THE FOREST-STEPPE OF UKRAINE
Authors: Dolia Mykola , Kovalska Anna 
Published: February 2021

The research aim is to improve the system of chickpea protection from pests, based on clarification of their specific composition and harmfulness under conditions of Forest-Steppe of Ukraine.
In modern field crop rotations leguminous crops cultivation favors optimization of the phytosanitary condition of agrocoenosis, and new agrarian production is provided by the effective demand for grain at not only internal, but also external markets. At that climate changes with global warming and long droughty vegetation periods of leguminous crops testify to the importance of searching for new adapted crops, resistant sorts and improved technological cultivation methods of crops, especially, chickpea, essentially influencing grain economy in whole both in Ukraine and EU.
Thus, it has been established, that ordinary chickpea (Cicer arietinum L.) is an economically, phytomedically and ecologically expedient crop from both aspects of soil fertility increase and control of the harmful organisms complex that, in its turn, it worth special attention, so sowing areas, occupied by it, are completely important. Soil-climatic conditions of Ukraine are optimal for cultivating native highly productive chickpea sorts, not inferior to foreign ones with the potential yielding capacity as 2.5–3.0 t/ha.
The authors elucidate one of main control peculiarities of the insects-phytophagans under new agriculture systems. It is typical, that chickpea is a comparatively new crop in the Forest-steppe of Ukraine and doesn’t favor the development, propagation and number increase of specialized pests’ species. It is noted, that due to fluffing and extraction of organic acids by leaves, chickpea manifests protective properties as to pests of leaves and generative organs. But chickpea is damaged by polyphagans with harvest losses in several variants up to 50% that testifies to the elaboration topicality of modern system of crops protection from phytophagans at resource-saving cultivation technologies
INVESTIGATION OF HYGROSCOPIC PROPERTIES AND POROSITY OF GLUED REINFORCED SAUSAGE CASINGS
Authors: Оnishchenko Vyacheslav , Pak Andrey , Goralchuk Andrii , Shubina Lidiia , Bolshakova Viktoria , Inzhyyants Samvel , Pak Alina , Domanova Olena 
Published: February 2021

There is substantiated the topicality of studying hygroscopic properties and porosity of glued reinforced sausage casings of intestinal raw materials. The work aim is to establish storage conditions of glued reinforced sausage casings of intestinal raw materials and their porosity determination. Studies of hygroscopic properties of glued reinforced sausage casings of intestinal raw materials have established a possibility of their long-term storage in a polymer package at a relative humidity no more 60…70 %. It has been established, that at a relative humidity more 70 %, storage is possible only in a steam-tight package. It has been noted, that a storage temperature at that must be selected in the diapason from 0 °С to 25 °С. It has been established, that the sorption isotherm for a model of a reinforcing seam material, obtained from glued intestinal casings using thermal coagulation, is lower than the one of the glued casing of intestinal raw materials relative to the axis of moisture content. The research result is explained by different porosity of samples. Differential functions of pores distribution by radiuses for studied samples have been obtained, and most probable and average radiuses for them have been calculated. The obtained distribution functions have a similar character and close maximum positions relative to the axis that the size-free pore radius is put on. They differ by lines width, testifying to the fact that samples differ by relative number of pores of different radiuses. It has been established, that most probable radiuses of pores for the studied samples differ within error, and average radiuses differ more than twice. It has been noted, that just more developed porous structure is a cause of the fact that the sorption isotherm of glued casings is higher relative to the one of a reinforcing seam material model. It has been noted, that at reinforcing protein molecules of the initial raw material change their structure because of thermal coagulation in such a way that the porous composition of the obtained raw material becomes closer to the monodispersed one
The atomic arrangement and electronic interactions in vonsenite at 295, 100, and 90 K
Authors: Maderazzo Marc , Hughes John M. , Dyar M. Darby , Rossman George R. , Ackley Brandon J. , Sklute Elizabeth C. , Lupulescu Marian V. , Chiarenzelli Jeffrey 
Published: February 2021

Abstract
Vonsenite, Fe22+Fe3+O2BO3, has been the subject of many studies in the materials science and condensed matter physics communities due to interest in the electronic and magnetic properties and ordering behavior of the phase. One such study, undertaken on synthetic material of end-member composition, reports X-ray diffraction structure refinements that indicate a phase transition from Pbam to Pbnm at or just below ~283 K, determined subsequently to arise from a Peierls-like instability. To compare the stability of the natural phase with that of synthetic material, we performed high-precision X-ray crystal-structure analyses at 295, 100, and 90 K (R1 = 0.0119, 0.0186, and 0.0183, respectively), Mössbauer spectroscopy at 295, 220, 150, 80, and 4.2 K, and wavelength-dispersive electron microprobe analysis on a vonsenite of near-end-member composition from Jayville, New York, U.S.A. The Pbnm structure is observed at 100 and 90 K, suggesting similar phase stability for the natural and synthetic phases. Comparison of Mössbauer data and X-ray site occupancies between the natural and synthetic phases suggests a reinterpretation of Mössbauer site assignments. We conclude that the Peierls-like instability underlying the reported transition from Pbam to Pbnm in synthetic material also occurs in our specimen of natural near-end-member vonsenite at temperatures between 295 and 100 K.
Mesoproterozoic seafloor authigenic glauconite-berthierine: Indicator of enhanced reverse weathering on early Earth
Authors: Ma Jianbai , Shi Xiaoying , Lechte Maxwell , Zhou Xiqiang , Wang Zhenfei , Huang Kangjun , Rudmin Maxim , Tang Dongjie 
Published: February 2021

Abstract
Sedimentary records suggest that the mid-Proterozoic (ca. 1.8–0.8 Ga) was persistently characterized by a greenhouse climate despite significantly lower solar luminosity compared to modern levels. To maintain greenhouse conditions, the partial pressure of carbon dioxide (pCO2) must have remained elevated, possibly indicative of key differences in the complexities of the carbon cycle compared to the modern. Modeling has suggested that high pCO2 was likely maintained by elevated rates of “reverse weathering:” marine authigenic clay formation, a process that consumes alkalinity and generates CO2. This process is kinetically slow in modern marine environments, yet is hypothesized to have been enhanced during the mid-Proterozoic due to the greater availability of important species for clay authigenesis such as silica and ferrous iron. This hypothesis is testable using the geological record, because enhanced reverse weathering would lead to the formation of abundant marine authigenic clays. However, the distribution of marine authigenic clays in the Proterozoic sedimentary record has not been paid sufficient attention. In this study, we report the presence of authigenic clays (glauconite and berthierine) from the Xiamaling Formation (ca. 1.4 Ga), North China. The glauconite-berthierine horizons occur as millimeter-to centimeter-thick laminae interbedded with muddy siltstone and feature detrital grains supported by the clay matrix. In places, these layers were partially reworked to form soft and cohesive intraclastic sands, suggesting a syndepositional origin. We hypothesize that marine iron cycling in the iron- and silica-rich mid-Proterozoic oceans may have facilitated the formation of authigenic iron-rich clay during the deposition of the Xiamaling Formation. The formation of iron-hydroxides on the seafloor—and the local increase in pH caused by subsequent dissimilatory iron reduction—could have resulted in the absorption of SiO2, Al(OH)3, and Fe(OH)2 to form soft, cohesive and noncrystalline Fe(OH)3-SiO2-Al(OH)3-Fe(OH)2 gels. These gels would have subsequently converted to glauconite/berthierine through aging. The transformation from glauconite-rich layers to berthierine-rich laminae was likely facilitated by a greater availability of Fe(II), and therefore higher Fe(II)/TFe and Fe/Si ratios. We suggest that the relatively rapid formation of syndepositional, seafloor berthierine and glauconite layers in the basal Xiamaling Formation is the result of enhanced reverse weathering during this time. This study provides an important geological support for carbon cycle models that invokes enhanced reverse weathering rates in the mid-Proterozoic ocean that may have helped to maintain a high-baseline pCO2 during this time.
On quantum separation of variables beyond fundamental representations
Authors: Maillet Jean Michel , Niccoli Giuliano 
Published: February 2021

We describe the extension, beyond fundamental representations of the
Yang-Baxter algebra, of our new construction of separation of variables
bases for quantum integrable lattice models. The key idea underlying our
approach is to use the commuting conserved charges of the quantum
integrable models to generate bases in which their spectral problem is separated,
i.e. in which the wave functions are factorized in terms of specific
solutions of a functional equation. For the so-called “non-fundamental”
models we construct two different types of SoV bases. The first is given
from the fundamental quantum Lax operator having isomorphic auxiliary
and quantum spaces and that can be obtained by fusion of the original
quantum Lax operator. The construction essentially follows the one we
used previously for fundamental models and allows us to derive the
simplicity and diagonalizability of the transfer matrix spectrum. Then,
starting from the original quantum Lax operator and using the full tower
of the fused transfer matrices, we introduce a second type of SoV bases
for which the proof of the separation of the transfer matrix spectrum is
naturally derived. We show that, under some special choice, this second
type of SoV bases coincides with the one associated to Sklyanin’s
approach. Moreover, we derive the finite difference type (quantum
spectral curve) functional equation and the set of its solutions
defining the complete transfer matrix spectrum. This is explicitly
implemented for the integrable quantum models associated to the higher
spin representations of the general quasi-periodic
Y(gl_{2})Y(gl2)
Yang-Baxter algebra. Our SoV approach also leads to the construction of
a QQ-operator
in terms of the fused transfer matrices. Finally, we show that the
QQ-operator
family can be equivalently used as the family of commuting conserved
charges enabling to construct our SoV bases.
Statistical analysis of fine resolution flow datasets helps characterizing flow behaviour in primary clarifiers: a decision support method
Authors: Kiss Katalin , Patziger Miklós 
Published: February 2021

Abstract
In situ measurement campaigns of primary clarifiers are rarely implemented properly because of their cost, time, and energy demand. Hydrodynamic modelling possibilities for such reactors have been intensely examined recently, but on-site factors affecting flow characteristics (e.g. flow distributors) have not received sufficient attention. This paper describes the use of ANOVA in examining fine resolution flow datasets and the related decision support method for in situ measurement campaigns and subsequent modelling processes. The characteristics of the flow and the applicability of 2D and 3D methods to investigate hydrodynamic features are discussed through the example of a rectangular primary clarifier, also considering the reproducibility of measurements ranging from typical nominal flow rates to peak loads. Based on the data, recommendations are provided on the adequate sizing of a measurement campaign, potentially reduced to a single longitudinal section (2D measurement). According to our results, performing hydrodynamic measurements with a 2D-arrangement of measuring points is sufficient in the case of such clarifiers, also with regard to the design processes. When applying the described methods, the related efforts and costs may be reduced and estimated more easily. However, care should be taken when applying this method to determine the spacing of measuring points correctly.
Development of Novel Rhodacyanine-Based Heat Shock Protein 70 Inhibitors
Authors: Chang Chih-Shiang , Kumar Vathan , Lee Der-Yen , Chen Yeh , Wu Yu-Chieh , Gao Jing-Yan , Chu Po-Chen 
Published: February 2021

Background:
A growing body of evidence suggests that Hsp70, which is overexpressed
in human breast tumors, plays a role in tumorigenesis and tumor progression
in breast cancer as well as in its aggressive phenotypes. Hsp70 constitutes a potential therapeutic
target in the treatment of this disease.

Methods:
We developed a new series of rhodacyanine-based Hsp70 inhibitors, represented
by compounds 1 and 6, in which the cationic pyridin-1-ium or thiazol-3-ium ring of
existing Hsp70 inhibitors (e.g., JG-40 and JG-98) was replaced by a corresponding benzo-
fused N-heterocycle.

Results:
Several lines of evidence suggest that these benzo-fused derivatives may exert
their antitumor activities, in part, by targeting Hsp70. These putative inhibitors displayed
differential antiproliferative efficacy against breast cancer cells (IC50 as low as 0.25 μM)
versus nontumorigenic MCF-10A breast epithelial cells (IC50 ≥ 5 μM). This was correlated
with the corresponding Hsp70 expression levels. Using a protein refolding assay, we
confirmed that these agents effectively inhibited the chaperone activity of Hsp70. Moreover,
these inhibitors effectively suppressed the expression of well-known oncogenic
client proteins of Hsp70’s, including FoxM1, HuR, and Akt, which paralleled their antiproliferative
efficacy. Supporting the established role of Hsp70 in regulating protein refolding,
these derivatives induced autophagy, as manifested by the conversion of LC3B-I
to LC3B-II. Notably, these putative Hsp70 inhibitors did not cause a compensatory elevation
in Hsp90 expression, contrasting with the previously reported effects of Hsp90 inhibitors
on Hsp70 upregulation.

Conclusion:
Together with the finding that compounds 1 and 6 showed improved microsomal
stability, these results suggest the translational potential of these putative Hsp70 inhibitors
to foster new strategies for cancer therapy. However, whether these benzo-fused
rhodacyanines act on kinases or other targets remains unclear. It is currently under investigation.