Separation Of Fragments Research Articles

MALDI-TOF Mass Spectrometry as the Tool for the Identification of Features of Polymers Obtained by Inverse Vulcanization

The MALDI-TOF mass-spectrometry was employed to analyze the structure of the reaction products of limonene, a natural terpene, and elemental sulfur, with the objective of identifying the occurrence of side processes, such as oxidative dehydrogenation, aromatization, and the Diels–Alder reaction cascade. The MALDI-TOF mass-spectrometry was demonstrated to be effective for the analysis of high-sulfur polymers obtained by the inverse vulcanization reaction, allowing for the unambiguous separation of sulfur-containing and hydrocarbon molecular fragments and the detailed characterization of macromolecular structures. By varying the ratio of sulfur (S8) and limonene in the initial reaction system, we were able to ascertain the limiting amount of sulfur that can be covalently bonded by terpene, as well as determine the average length of polysulfide chains under the assumption of equal reactivity and complete depletion of all double bonds. The side reaction of limonene aromatization, as indicated by the MALDI-TOF spectrum of the product resulting from its interaction with elemental sulfur, was corroborated by 1H and 13C NMR spectroscopy. Consequently, the registration and interpretation of MALDI-TOF spectra of inverse vulcanization products, either independently or in conjunction with the application of 1H and 13C NMR spectroscopy methods, as well as the determination of the limiting number of sulfur atoms that can be bound to one molecule of an unsaturated compound, paves the way for new avenues of investigation into the structure and side reactions involved in the synthesis of high-sulfur polymers.

Engineered protein destabilization reverses intrinsic immune evasion for candidate vaccine pan-strain KSHV and SARS-CoV-2 antigens.

Both Kaposi sarcoma herpesvirus LANA and SARS coronavirus 2 RdRp/nsp12 are highly conserved replication proteins that evade immune processing. By deleting the LANA central repeat 1 domain (LANA ΔCR1 ) or by dividing RdRp into two separated fragments (RdRp Frag ) to maximize nascent protein mis-folding, cis peptide presentation was increased. Native LANA or RdRp SIINFEKL fusion proteins expressed in MC38 cancer cells were not recognized by activated OT-1 CD8 + cells against SIINFEKL but cytotoxic recognition was restored by expression of the corresponding modified proteins. Immunocompetent syngeneic mice injected with LANA- or RdRp-SIINFEKL MC38 cells developed rapidly-growing tumors with short median survival times. Mice injected with LANA ΔCR1 - or RdRp Frag -SIINFEKL had partial tumor regression, slower tumor growth, longer median survival, as well as increased effector-specific tumor-infiltrating lymphocytes. These mice developed robust T cell responses lasting at least 90 days post-injection that recognized native viral protein epitopes. Engineered vaccine candidate antigens can unmask virus-specific CTL responses that are typically suppressed during native viral infection.

Management of Intracanal Separated Instruments Using Ultrasonics: A Case Series

Cleaning and shaping of the root canal system is an important step in non-surgical endodontic treatment. One of the mishaps associated with this step is intracanal instrument separation. Endodontic instruments separation often results from overuse or incorrect use. Such an event impedes shaping, disinfection and subsequent filling of the canal space apical to the instrument fragment. The use of ultrasonics has shown appreciable success for management of these cases especially when supported with magnification and illumination. With adequate knowledge, suitable armamentaria, fine clinical skills, and experience successful management of such cases, without further complications, is possible. If not well managed, intracanal separated instrument fragments adversely affect the long-term treatment outcome of endodontically treated teeth. This report presents three cases with intracanal separated instruments which were successfully managed with the use of ultrasonics under magnification with dental loupes. Keywords: Instrument Separation, Retrieval, Root Canal Treatment, Ultrasonics

A charge reversal approach for the sensitive quantification of dicarboxylic acids using Liquid chromatography-tandem mass spectrometry

Dicarboxylic acids (DCAs) are essential for intermediate metabolism and are implicated in multiple processes associated with various diseases. Several DCAs contribute to energy metabolism, impact mitochondrial function, and play a crucial role in body function. However, the low abundance of some DCAs in various body fluids makes their quantification particularly challenging. Therefore, an extremely sensitive method is required to determine DCA level fluctuations in biological samples in different diseases. We developed and optimized an LC-MS/MS method to quantify DCAs. We achieved charge reversal of the compounds from negative to positive ionization through chemical derivatization with dimethylaminophenacyl bromide (DmPABr) targeting the carboxyl group (R-COOH) under mild basic conditions. Derivatization enhanced sensitivity, mass fragmentation, and chromatographic separation for LC-tandem mass spectrometric quantification. The method was analytically optimized and demonstrated excellent linearity for individual DCAs (R2>0.99), as well as an exceptionally lower limit of detection (LLOD<266 fg) and lower limit of quantification (LLOQ<805 fg) for all DCAs. Furthermore, most derivatized DCAs were stable at room temperature and after ten repeated freeze−thaw cycles. After DCA extraction and quantification detection, we found differences in their distribution in plasma and urine. The rank order for DCAs in plasma is C4>C6>C7>C9>C5>C8>C22, whereas in the urine sample, the order is C4>C7>C6>C9>C5>C8>C10. For longer chains (C > 16), their proportions were >10x higher in plasma than in urine. Our optimized method using LC-MS/MS enables the quantification of DCAs with excellent sensitivity. The method will help in future studies investigating dicarboxylic acids' crucial role in health and biomarker discovery studies using targeted metabolomics.

Partitioning behavior of short DNA fragments in polymer/salt aqueous two-phase systems.

The development of liquid biopsy as a minimally invasive technique for tumor profiling has created a need for efficient biomarker extraction systems from body fluids. The analysis of circulating cell-free DNA (cfDNA) is especially promising, but the low amounts and high fragmentation of cfDNA found in plasma pose challenges to its isolation. While the potential of aqueous two-phase systems (ATPS) for the extraction and purification of various biomolecules has already been successfully established, there is limited literature on the applicability of these findings to short cfDNA-like fragments. This study presents the partitioning behavior of a 160 bp DNA fragment in polyethylene glycol (PEG)/salt ATPS at pH 7.4. The effect of PEG molecular weight, tie-line length, neutral salt additives, and phase volume ratio is evaluated to maximize DNA recovery. Selected ATPS containing a synthetic plasma solution spiked with human serum albumin and immunoglobulin G are tested to determine the separation of DNA fragments from the main plasma protein fraction. By adding 1.5% (w/w) NaCl to a 17.7% (w/w) PEG 400/17.3% (w/w) phosphate ATPS, 88% DNA recovery was achieved in the salt-rich bottom phase while over 99% of the protein was removed.

Study on aluminum recovery from selected aluminum-containing packaging waste by pyrolysis system

Abstract Nowadays, consumers more frequently than not choose packaged food over fast food due to its convenience, high nutrition value, ease of preparation, and health friendliness. This has caused the amount of packaging waste in the world to increase rapidly, becoming one of the major dangers to the global environment. The potential hazard associated with this kind of waste and have been developing more innovative techniques to lessen its negative impacts. This study aims to convert food packaging wastes (FPWs) into raw materials (aluminum and carbon particles) using three combined methods: pyrolysis, mechanical and chemical treatment. This experiment used a furnace used in the laboratory to heat plastic packaging waste to obtain a solid fraction, under pre-set conditions, including temperatures of 500 °C, 600 °C, 700 °C, and 800 °C, and the retention time is 10 min, 20 min, 30 min. Specifically, the highest amount of solid fraction obtained was 20.9% at the condition of 500°C for 10 minutes, while the recovery rate was the lowest at 8.91% at the condition of 800 °C for 30 minutes. According to the references, the retention time condition of 30 minutes is the optimum for aluminum recovery, of which 800°C is the best with 8.11%, along with the ease of separation of aluminum fragments and aluminum particles out of the mixture. Finally, Fourier transform infrared spectroscopy (FTIR) analysis was used to confirm the composition of the solid obtained after the pyrolysis process, the selected wavelength ranged from 650-4000 cm−1. In summary, the experiment was successful when it found the optimal conditions for the pyrolysis method in recovering aluminum from packaging waste. In addition, the recovery of aluminum metal from this type of waste also contributes to solving the very high demand for this metal in recent times.

A compact ion source combining electron-impact and thermal ionization for multiple-reflection time-of-flight mass spectrometry.

A compact ion source combining electron impact and thermal ionization has been developed and commissioned in two Multiple-Reflection Time-Of-Flight Mass Spectrometer (MR-TOF-MS) setups at the Fragment Separator Ion Catcher at the GSI Helmholtz Centre for Heavy Ion Research, Darmstadt, Germany, and at TRIUMF's Ion Trap for Atomic and Nuclear science at TRIUMF Canada's particle accelerator center, Vancouver, Canada. The ion source is notable for its compact dimensions of 50mm in height and 68mm in diameter. The ion source is currently in daily operation at both facilities. Design, simulations, and results of combining ions from thermal and electron-impact ionization of different gases (perfluoropropane and sulfur hexafluoride) are presented in this work. The systematic effects of heating power on the thermal source were studied in detail. The source has demonstrated stable and long-term production of reference ions over a wide mass range for the MR-TOF-MS. This versatile ion source has also been used to optimize and investigate the transport of ions with different chemical reactivity and ionization potentials.

Evaluation of Magnetic Performance of Superconducting Magnets for the Superconducting Fragment Separator at FAIR

Evaluation of Magnetic Performance of Superconducting Magnets for the Superconducting Fragment Separator at FAIR

Mechanical Design, Construction and Testing of the Superferric Dipoles for the High Energy Fragment Separator of the HIAF

Mechanical Design, Construction and Testing of the Superferric Dipoles for the High Energy Fragment Separator of the HIAF

Study on the influence of landscape pattern on the spread of pine wilt disease from a multi-scale perspective

Since the introduction of pine wilt disease (PWD) into Chongqing, China, it has been continuously spreading, posing a significant threat to the local forest ecosystem dominated by pine forests. Utilizing data spanning the last two decades on the PWD epidemic subcompartment and host coniferous forest in Chongqing, this study employs a geographic detector model to scrutinize the impact of forest landscape patterns on PWD dissemination at the county, township, and 1 km grid scales. The findings reveal three distinct stages of the PWD epidemic in Chongqing from 2001 to 2020: diffusion, stabilization, and outbreak. The western and central regions of Chongqing experienced severe impacts, while the southern part exhibited relatively milder effects. Across the three spatial scales, various landscape pattern indices exhibit robust and consistent impacts on PWD occurrence. Notably, patch area emerges as the most influential factor, with an explanatory power reaching 0.228. Additionally, landscape shape index, number of patches, patch density, river and road exert substantial influence on PWD incidence. Conversely, the impact of edge density, landscape dominance, landscape separation, and landscape fragmentation on PWD occurrence is comparatively weak. Moreover, the interaction of different landscape pattern factors nonlinearly enhances the explanatory power of PWD occurrence. Among these interactions, the synergy between patch area and landscape dominance proves to have the highest explanatory power for the spatial differentiation of PWD at 0.718. This study explores the relationship between the invasion and spread of PWD and landscape patterns, offering useful insights for the prevention and early warning of PWD. Additionally, this research provides valuable reference points for promoting the healthy and sustainable development of forest resources in China.

Rhesus Macaques: VNTR Polymorphism of the FCGRT Gene.

Variable number tandem repeat (VNTR) polymorphisms of the human neonatal IgG Fc receptor α-chain gene (FCGRT) are known to influence the expression levels of FCGRT and IgG in serum. Monkeys are considered to be a relevant biological model for studying the effects of immunobiological drugs. The study determined the functional VNTR polymorphisms of the FCGRT gene in 109 male rhesus macaques from the nursery of the Kurchatov Complex of Medical Primatology. PCR amplification of samples was carried out followed by electrophoretic separation of DNA fragments in a 2% agarose gel. Individual DNA amplification products were sequenced (according to Sanger system) in forward and reverse directions to confirm the specificity. The genotyping showed that the VNTR polymorphism of the FCGRT gene in the studied population of rhesus macaques is presented by 9 variants. The frequency of the VNTR5 allele associated with lower IgG levels was 14.2%, and the most common one was the VNTR7 allele (25.2%). We also identified alleles that have not been previously reported: VNTR3, VNTR4, VNTR6, VNTR8, and VNTR9. The study allows to consider rhesus macaques as a potential model for studying the immunological response depending on the genetic VNTR variant of FCGRT.

Nuclear structure opportunities with GeV radioactive beams at FAIR.

The Facility for Antiproton and Ion Research (FAIR) is in its final construction stage next to the campus of the Gesellschaft für Schwerionenforschung Helmholtzzentrum for heavy-ion research in Darmstadt, Germany. Once it starts its operation, it will be the main nuclear physics research facility in many basic sciences and their applications in Europe for the coming decades. Owing to the ability of the new fragment separator, Super-FRagment Separator, to produce high-intensity radioactive ion beams in the energy range up to about 2 GeV/nucleon, these can be used in various nuclear reactions. This opens a unique opportunity for various nuclear structure studies across a range of fields and scales: from low-energy physics via the investigation of multi-neutron systems and halos to high-density nuclear matter and the equation of state, following heavy-ion collisions, fission and study of short-range correlations in nuclei and hypernuclei. The newly developed reactions with relativistic radioactive beams (R3B) set up at FAIR would be the most suitable and versatile for such studies. An overview of highlighted physics cases foreseen at R3B is given, along with possible future opportunities, at FAIR. This article is part of the theme issue 'The liminal position of Nuclear Physics: from hadrons to neutron stars'.

A Codicological Analysis of the Judeo-Persian Sefer Ha-Melitza Dictionary (Evr. I 75–76) from the Collection of the National Library (St. Petersburg)

The article presents a codicological analysis of the medieval Judeo-Persian dictionary Sefer ha-Melitsa. Two items in the NLR collection, Evr.I75 (a volume) and 76 (separate fragments), can be divided into two separate manuscripts: the first manuscript is a codex dated back to 1340 and the latter seems to be a later manuscript, which was used as a restoration of the first one’s losses, at first glance. However, a detailed analysis of the text structure suggests that the two manuscripts existed independently, since they repeat each other’s texts. Given the codicology of the monuments and the text of the colophon (f.87a), we can assume that we are dealing with a copy of the original work, but, unfortunately, not with the autograph of the medieval dictionary.

Analysis of load distribution after transpedicular stabilization of burst fractures in the thoracolumbar junction

Background. In the structure of all traumatic spine injuries, the thoracolumbar junction is predominant, accounting for over 53 % of all vertebral fractures. One of the most clinically significant types of injuries in this area are burst fractures. The purpose was to study the stress-strain state of the thoracolumbar spine model with a burst fracture of the Th12 vertebra in various transpedicular fixation options under compression load. Materials and methods. The study developed and investigated a finite element model of the thoracolumbar spine with a burst fracture of the Th12 vertebra. The burst fracture was modeled by dividing the vertebral body of the Th12 into several planes, transforming it into separate fragments. The gaps between these fragments were filled with a material that simulated the interfragmentary regenerate. Variants of transpedicular stabilization using different types of screws, mono- or bicortical, and with or without cross-links, were examined. The model was analyzed under compression load. Results. The maximum level of stress among the bone structures directly involved in fixation was registered in the L2 vertebral body. It amounted to 19.9, 15.6, 19.4, and 15.1 MPa, respectively, for models with monocortical screws without cross-links, bicortical screws without cross-links, monocortical screws with cross-links, bicortical screws with cross-links. Simultaneously, the zone of screw entry into the arch of this vertebra shows values of 10.1, 15, 10.2, and 14.3 MPa for these models, respectively. Peak loads on the metal structure elements are observed on the rods, amounting to 212.5, 159.6, 203.7, 142.8 MPa, respectively, for the considered models. Conclusions. The results of the study showed that under the influence of compression load when modeling a burst fracture of the thoracolumbar junction, the use of long screws leads to a reduction in stress levels, both in the elements of the metal structure and in the bone elements of the model, while the use of cross-links has a negligible effect.

Process design for FRIB’s experimental refrigeration system

The experimental system (ES) for the Facility for Rare Isotope Beams (FRIB) at Michigan State University (MSU) has several segments. Following the acceleration through the three superconducting LINAC segments, the heavy ion beam is guided through the target, a fragment pre-separator and (the A1900) separator segments. There are many beam lines and then it can be split and sent to various experimental vaults and instrumentation, e.g. S800 spectrograph, and the newly proposed High Rigidity Spectrometer (HRS). Presently, superconducting magnets at the target and fragment pre-separator segments, along with the LINAC superconducting cryo-modules, are supported by FRIB’s main central helium liquefier/refrigerator (CHL). The remainder of the cryogenic loads are supported by the legacy NSCL Cryogenic Refrigerator (a re-commissioned Bureau of Mines helium liquefier from the mid 1970’s) and has many obsolete components for reliable operation. Considering the operational reliability of the accelerator, maintainability of the entire cryogenic system at FRIB and ever-growing experimental beam lines – it is logical to segregate the experimental system loads from the accelerator system loads. A new 4.5 K refrigerator along with a thermal shield (55 K) refrigerator are planned to support the operation of these experimental system (ES) loads and make plans for the CHL maintenance. These refrigerators will be able to support a combination of 4.5 K isothermal refrigeration, 4.5 K liquefaction (for magnet lead cooling and transients) and thermal radiation shield loads. The design loads, modes of operation and the planned operation of the FRIB cryogenic system with these refrigeration systems are discussed. This paper outlines the key selection parameters and design modes for the major components, such as the warm compressors, turbo-expanders and heat exchangers.

Conceptual design and simulated performance of the Barrel part of gamma array for the experimental terminal at HFRS of HIAF

The Barrel of γ array, consisting of 640 CsI(Tl) crystals and covering a polar angle range from 36.4° to 135.6°, has been designed for the experimental terminals at High energy FRagment Separator of High-Intensity heavy-ion Accelerator Facility in Huizhou. Together with the existing Endcap, consisting of 1024 CsI(Tl) crystals and covering a polar angle from 15.6° to 36.4°, at the External Target Facility in Lanzhou to form a new γ array, it is expected to meet the experimental requirements for in-beam γ-ray spectroscopy technique. A Monte Carlo code based on Geant4 was implemented to study the performance of the new γ array. Taking into account the Doppler correction and the intrinsic energy resolution of the detector, the energy resolution is 5.4% (FWHM) for the Endcap and 9.8% (FWHM) for the Barrel when the energy of the emitted γ-ray is 1 MeV in the Center-of-Mass frame with the beam energy of 500 MeV/u (beam velocity β = 0.759). The full-space photopeak efficiency is greater than 40% when the energy of the emitted γ-ray is less than 5 MeV in the Center-of-Mass frame and the beam energy is less than 700 MeV/u (β = 0.821). Such performance can satisfy most of the physics requirements for in-beam γ-ray spectroscopy experiments.

Parallel-plate avalanche counters for heavy-ion beam tracking: History and mysteries

Despite being an old detector concept, position-sensitive parallel-plate avalanche counters (PPACs) remain widely used today for heavy-ion position and timing measurements. In modern rare isotope beam facilities and large-acceptance fragment separators, PPACs are used to characterize beam properties (diagnostics), facilitate beam delivery (tuning), and provide event-by-event beam tracking for particle identification (PID). Most popular particle localization methods in PPAC detectors are based on strip electrodes electrically connected to resistive-chain circuits or delay lines. More exotic systems include optical readouts based on recording electroluminescence light with high-granularity photodetector arrays or high-resolution resistive anode electrodes. PPACs with conventional resistive-chain or delay-line readouts achieve typical position and time resolutions of below 1 mm (σ) and around 150 ps (σ), respectively. In addition, delay-line systems are capable of counting rates above several hundred kHz for beam areas of a few millimeters square, and around 1 MHz for larger beam sizes. Resistive-chain readouts have limited rates of a few tens of kHz. A review of the operation principles and performance of PPAC detectors is presented in this paper. We will discuss decades-long experience building and operating PPACs developed at the National Superconducting Cyclotron Laboratory, and then refined at the Facility for Rare Isotope Beams (FRIB), mostly focusing on the delay-line readout technique (DLPPAC). We will also discuss problems that arise due to electric discharges at high rates and briefly describe ongoing developments at FRIB. Published by the American Physical Society 2024

Chemical Proteomics Strategies for Analyzing Protein Lipidation Reveal the Bacterial O-Mycoloylome.

Protein lipidation dynamically controls protein localization and function within cellular membranes. A unique form of protein O-fatty acylation in Corynebacterium, termed protein O-mycoloylation, involves the attachment of mycolic acids─unusually large and hydrophobic fatty acids─to serine residues of proteins in these organisms' outer mycomembrane. However, as with other forms of protein lipidation, the scope and functional consequences of protein O-mycoloylation are challenging to investigate due to the inherent difficulties of enriching and analyzing lipidated peptides. To facilitate the analysis of protein lipidation and enable the comprehensive profiling and site mapping of protein O-mycoloylation, we developed a chemical proteomics strategy integrating metabolic labeling, click chemistry, cleavable linkers, and a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method employing LC separation and complementary fragmentation methods tailored to the analysis of lipophilic, MS-labile O-acylated peptides. Using these tools in the model organism Corynebacterium glutamicum, we identified approximately 30 candidate O-mycoloylated proteins, including porins, mycoloyltransferases, secreted hydrolases, and other proteins with cell envelope-related functions─consistent with a role for O-mycoloylation in targeting proteins to the mycomembrane. Site mapping revealed that many of the proteins contained multiple spatially proximal modification sites, which occurred predominantly at serine residues surrounded by conformationally flexible peptide motifs. Overall, this study (i) discloses the putative protein O-mycoloylome for the first time, (ii) yields new insights into the undercharacterized proteome of the mycomembrane, which is a hallmark of important pathogens (e.g., Corynebacterium diphtheriae, Mycobacterium tuberculosis), and (iii) provides generally applicable chemical strategies for the proteomic analysis of protein lipidation.

Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21.

Endosomal trafficking ensures the proper distribution of lipids and proteins to various cellular compartments, facilitating intracellular communication, nutrient transport, waste disposal, and the maintenance of cell structure. Retromer, a peripheral membrane protein complex, plays an important role in this process by recruiting the associated actin-polymerizing WASH complex to establish distinct sorting domains. The WASH complex is recruited through the interaction of the VPS35 subunit of retromer with the WASH complex subunit FAM21. Here, we report the identification of two separate fragments of FAM21 that interact with VPS35, along with a third fragment that binds to the VPS29 subunit of retromer. The crystal structure of VPS29 bound to a peptide derived from FAM21 shows a distinctive sharp bend that inserts into a conserved hydrophobic pocket with a binding mode similar to that adopted by other VPS29 effectors. Interestingly, despite the network of interactions between FAM21 and retromer occurring near the Parkinson's disease-linked mutation (D620N) in VPS35, this mutation does not significantly impair the direct association with FAM21 in vitro.

Stability indicating ion-pair reversed-phase liquid chromatography method for modified mRNA

Modified messenger RNA (mRNA) represents a rapidly emerging class of therapeutic drug product. Development of robust stability indicating methods for control of product quality are therefore critical to support successful pharmaceutical development. This paper presents an ion-pair reversed-phase liquid chromatography (IP-RPLC) method to characterise modified mRNA exposed to a wide set of stress-inducing conditions, relevant for pharmaceutical development of an mRNA drug product. The optimised method could be used for separation and analysis of large RNA, sized up to 1000 nucleotides. Column temperature, mobile phase flow rate and ion-pair selection were each studied and optimised. Baseline separations of the model RNA ladder sample were achieved using all examined ion-pairing agents. We established that the optimised method, using 100 mM Triethylamine, enabled the highest resolution separation for the largest fragments in the RNA ladder (750/1000 nucleotides), in addition to the highest overall resolution for the selected modified mRNA compound (eGFP mRNA, 996 nucleotides). The stability indicating power of the method was demonstrated by analysing the modified eGFP mRNA, upon direct exposure to heat, hydrolytic conditions and treatment with ribonucleases. Our results showed that the formed degradation products, which appeared as shorter RNA fragments in front of the main peak, could be well monitored, using the optimised method, and the relative stability of the mRNA under the various stressed conditions could be assessed.