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- Bing, Li, et al.
(författare)
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Design of Auto-Configurable Random Access NOMA for URLLC Industrial IoT Networking
- 2024
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Ingår i: IEEE Transactions on Industrial Informatics. - 1941-0050 .- 1551-3203. ; 20:1, s. 190-200
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Tidskriftsartikel (refereegranskat)abstract
- Low power devices are massively deployed to facilitate real time sensing and data transmission requested in low power wide-area network (LPWAN). However, the dominating signaling, i.e. continuous phase modulation (CPM), barely gains attention in the context of supporting massive connectivity, not to mention ultra-reliable low-latency communications (URLLC), a primary concern in industrial network automation. To this end, auto-configurable nonorthogonal multiple access (AC-NOMA) based on CPM signaling is proposed. The term auto-configuration is used since each device selects a setup from a pool of configurations whenever connecting to the access point in a random and distributive way. It is proven, using ideal power allocation and phase shaping technique, AC-NOMA offers drastically improved user load and near capacity performance even in finite blocklength regime. Moreover, to enable massive yet sporadic access, slotted ALOHA is combined with AC-NOMA. It is proven that the resultant scheme outperforms power-domain NOMA in terms of throughput even with reduced transmit power and simple forward error correction schemes such as repetition and convolutional coding. The throughput is further improved using semi AC-NOMA with slightly increased latency. It is demonstrated that both designs can support very high user load while enabling URLLC in finite blocklength regime, where the packet size is merely 256 bits while the error rate is $10^{-5}$, which are also desirable in a number of applications including satellite communications, visible light communications, etc.
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| 4. |
- Blalock, Zachary N., et al.
(författare)
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Circulating cell-free mitochondrial DNA levels and glucocorticoid sensitivity in a cohort of male veterans with and without combat-related PTSD
- 2024
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Ingår i: Translational Psychiatry. - 2158-3188. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Circulating cell-free mitochondrial DNA (ccf-mtDNA) is a biomarker of cellular injury or cellular stress and is a potential novel biomarker of psychological stress and of various brain, somatic, and psychiatric disorders. No studies have yet analyzed ccf-mtDNA levels in post-traumatic stress disorder (PTSD), despite evidence of mitochondrial dysfunction in this condition. In the current study, we compared plasma ccf-mtDNA levels in combat trauma-exposed male veterans with PTSD (n = 111) with those who did not develop PTSD (n = 121) and also investigated the relationship between ccf mt-DNA levels and glucocorticoid sensitivity. In unadjusted analyses, ccf-mtDNA levels did not differ significantly between the PTSD and non-PTSD groups (t = 1.312, p = 0.191, Cohen’s d = 0.172). In a sensitivity analysis excluding participants with diabetes and those using antidepressant medication and controlling for age, the PTSD group had lower ccf-mtDNA levels than did the non-PTSD group (F(1, 179) = 5.971, p = 0.016, partial η 2 = 0.033). Across the entire sample, ccf-mtDNA levels were negatively correlated with post-dexamethasone adrenocorticotropic hormone (ACTH) decline (r = −0.171, p = 0.020) and cortisol decline (r = −0.149, p = 0.034) (viz., greater ACTH and cortisol suppression was associated with lower ccf-mtDNA levels) both with and without controlling for age, antidepressant status and diabetes status. Ccf-mtDNA levels were also significantly positively associated with IC50-DEX (the concentration of dexamethasone at which 50% of lysozyme activity is inhibited), a measure of lymphocyte glucocorticoid sensitivity, after controlling for age, antidepressant status, and diabetes status (β = 0.142, p = 0.038), suggesting that increased lymphocyte glucocorticoid sensitivity is associated with lower ccf-mtDNA levels. Although no overall group differences were found in unadjusted analyses, excluding subjects with diabetes and those taking antidepressants, which may affect ccf-mtDNA levels, as well as controlling for age, revealed decreased ccf-mtDNA levels in PTSD. In both adjusted and unadjusted analyses, low ccf-mtDNA levels were associated with relatively increased glucocorticoid sensitivity, often reported in PTSD, suggesting a link between mitochondrial and glucocorticoid-related abnormalities in PTSD.
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- Cheng, Peifu, et al.
(författare)
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High-Performance Hemofiltration via Molecular Sieving and Ultra-Low Friction in Carbon Nanotube Capillary Membranes
- 2023
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Ingår i: Advanced Functional Materials. - 1616-301X. ; 33:50
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Tidskriftsartikel (refereegranskat)abstract
- Conventional dialyzer membranes typically comprise of unevenly distributed polydisperse, tortuous, rough pores, embedded in relatively thick ≈20–50 µm polymer layers wherein separation occurs via size exclusion as well as differences in diffusivity of the permeating species. However, transport in such polymeric pores is increasingly hindered as the molecule size approaches the pore dimension, resulting in significant retention of undesirable middle molecules (≥15–60 kDa) and uremic toxins. Enhanced removal of middle molecules is usually accompanied by high albumin loss (≈66 kDa) causing hypoalbuminemia. Here, the scalable bottom-up fabrication of wafer-scale carbon nanotube (CNT) membranes with highly aligned, low-friction, straight-channels/capillaries and narrow pore-diameter distributions (≈0.5–4.5 nm) is demonstrated, to overcome persistent challenges in hemofiltration/hemodialysis. Using fluorescein isothiocyanate (FITC)-Ficoll 70 and albumin in phosphate buffered saline (PBS) as well as in bovine blood plasma, it is shown that CNT membranes can allow for significantly higher hydraulic permeability (more than an order of magnitude when normalized to pore area) than commercial high-flux hemofiltration/hemodialysis membranes (HF 400), as well as greatly enhance removal of middle molecules while maintaining comparable albumin retention. These findings are rationalized via an N-pore transport model that highlights the critical role of molecular flexing and deformation during size-selective transport within nanoscale confinements of the CNTs. The unique transport characteristics of CNTs coupled with size-exclusion and wafer-scale fabrication offer transformative advances for hemofiltration, and the obtained insight into molecular transport can aid advancements in several other bio-systems/applications beyond hemofiltration/hemodialysis.
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- Gaca, Anthony O., et al.
(författare)
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From (p)ppGpp to (pp)pGpp : characterization of Regulatory Effects of pGpp Synthesized by the Small Alarmone Synthetase of Enterococcus faecalis
- 2015
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Ingår i: Journal of Bacteriology. - : American Society for Microbiology. - 0021-9193 .- 1098-5530. ; 197:18, s. 2908-2919
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Tidskriftsartikel (refereegranskat)abstract
- The bacterial stringent response (SR) is a conserved stress tolerance mechanism that orchestrates physiological alterations to enhance cell survival. This response is mediated by the intracellular accumulation of the alarmones pppGpp and ppGpp, collectively called (p) ppGpp. In Enterococcus faecalis, (p) ppGpp metabolism is carried out by the bifunctional synthetase/hydrolase E. faecalis Rel (Rel(Ef)) and the small alarmone synthetase (SAS) RelQ(Ef). Although Rel is the main enzyme responsible for SR activation in Firmicutes, there is emerging evidence that SASs can make important contributions to bacterial homeostasis. Here, we showed that RelQ(Ef) synthesizes ppGpp more efficiently than pppGpp without the need for ribosomes, tRNA, or mRNA. In addition to (p) ppGpp synthesis from GDP and GTP, RelQ(Ef) also efficiently utilized GMP to form GMP 3'-diphosphate (pGpp). Based on this observation, we sought to determine if pGpp exerts regulatory effects on cellular processes affected by (p) ppGpp. We found that pGpp, like (p) ppGpp, strongly inhibits the activity of E. faecalis enzymes involved in GTP biosynthesis and, to a lesser extent, transcription of rrnB by Escherichia coli RNA polymerase. Activation of E. coli RelA synthetase activity was observed in the presence of both pGpp and ppGpp, while RelQ(Ef) was activated only by ppGpp. Furthermore, enzymatic activity of RelQ(Ef) is insensitive to relacin, a (p) ppGpp analog developed as an inhibitor of "long" RelA/SpoT homolog (RSH) enzymes. We conclude that pGpp can likely function as a bacterial alarmone with target-specific regulatory effects that are similar to what has been observed for (p) ppGpp. IMPORTANCE Accumulation of the nucleotide second messengers (p) ppGpp in bacteria is an important signal regulating genetic and physiological networks contributing to stress tolerance, antibiotic persistence, and virulence. Understanding the function and regulation of the enzymes involved in (p) ppGpp turnover is therefore critical for designing strategies to eliminate the protective effects of this molecule. While characterizing the (p) ppGpp synthetase RelQ of Enterococcus faecalis (RelQ(Ef)), we found that, in addition to (p) ppGpp, RelQ(Ef) is an efficient producer of pGpp (GMP 3'-diphosphate). In vitro analysis revealed that pGpp exerts complex, target-specific effects on processes known to be modulated by (p) ppGpp. These findings provide a new regulatory feature of RelQ(Ef) and suggest that pGpp may represent a new member of the (pp) pGpp family of alarmones.
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| 7. |
- Golub, Koraljka, Professor, 1975-, et al.
(författare)
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Using ChatGPT for (semi-) automatic subject indexing of different document types
- 2024
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We are currently in a phase where it seems that new applications for large language models (LLMs) in general and generative pre-trained transformers (GPTs) in particular are tested every day. Examples are as diverse as automated data mining for building energy management (C. Zhang et al., 2024), evaluating the accuracy of differential-diagnosis lists for clinical vignettes (Hirosawa et al., 2023), and human-machine-augmented intelligent vehicles (J. Zhang et al., 2023). They can also be used to extract structured information from unstructured text (Söderström, 2023). This poster presents a pilot study on one such application, the potential use of OpenAI’s ChatGPT for automatic subject indexing of archival documents in Swedish, Swedish LGBTQ fiction and Chinese fiction. The accuracy of the assigned subject index terms is compared with the output from ANNIF (Suominen et al., 2022), an established automatic subject indexing software used in libraries. The results display an impressive degree of accuracy for the subject index terms assigned by ChatGPT, but challenges have been identified in all three document types. For example, the appropriateness of the terms for historical text is highly questionable at times. The terms assigned by ANNIF, in contrast, are drawn from a controlled vocabulary, which ensures that they have been manually selected as suitable subject index terms. The pilot study shows that it is feasible to run the index terms suggested by ChatGPT through ANNIF to get index terms from a controlled vocabulary while harnessing ChatGPT’s state-of-the-art natural language understanding. This presents intriguing opportunities for implementing GPTs in the archival/library cataloging workflows. Semi-automatic approaches and manual checks are still to be preferred, however, in order to maintain the authenticity of the generated metadata.
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| 8. |
- Hong, Junmei, et al.
(författare)
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Focusing on RISC assembly in mammalian cells.
- 2008
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Ingår i: Biochem Biophys Res Commun. - : Elsevier BV. - 1090-2104 .- 0006-291X. ; 368:3, s. 703-8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- RISC (RNA-induced silencing complex) is a central protein complex in RNAi, into which a siRNA strand is assembled to become effective in gene silencing. By using an in vitro RNAi reaction based on Drosophila embryo extract, an asymmetric model was recently proposed for RISC assembly of siRNA strands, suggesting that the strand that is more loosely paired at its 5' end is selectively assembled into RISC and results in target gene silencing. However, in the present study, we were unable to establish such a correlation in cell-based RNAi assays, as well as in large-scale RNAi data analyses. This suggests that the thermodynamic stability of siRNA is not a major determinant of gene silencing in mammalian cells. Further studies on fork siRNAs showed that mismatch at the 5' end of the siRNA sense strand decreased RISC assembly of the antisense strand, but surprisingly did not increase RISC assembly of the sense strand. More interestingly, measurements of melting temperature showed that the terminal stability of fork siRNAs correlated with the positions of the mismatches, but not gene silencing efficacy. In summary, our data demonstrate that there is no definite correlation between siRNA stability and gene silencing in mammalian cells, which suggests that instead of thermodynamic stability, other features of the siRNA duplex contribute to RISC assembly in RNAi.
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| 9. |
- Song, J., et al.
(författare)
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The association of severe anemia, red blood cell transfusion and necrotizing enterocolitis in neonates
- 2021
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 16:7
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Tidskriftsartikel (refereegranskat)abstract
- Background The relationship between severe anemia, red blood cell transfusion and Neonatal necrotizing enterocolitis (NEC) remains controversial. The purpose of this study was to determine the association of severe anemia and RBC transfusion with NEC in neonates. Methods The clinical characteristics of NEC were observed in 467 infants with different birth weights from January 2012 to July 2020. A 1:1 ratio case-control study was performed in very low birth weight (VLBW) infants. Severe anemia, RBC transfusion, and confounding factors, including maternal and perinatal complications, feeding, and antibiotics administration were collected in both groups. Univariate and multivariate analyses were used to investigate effects on the risk of NEC. Results The day of NEC onset and mortality were inversely associated with birth weight. In VLBW infants, adjusting for other factors, severe anemia within 72 h [OR = 2.404, P = 0.016], RBC transfusion within 24 h [OR = 4.905, P = 0.016], within 48 h [OR = 5.587, P = 0.008], and within 72 h [OR = 2.858, P = 0.011] increased the risk of NEC. Conclusion Both severe anemia and RBC transfusion appears to increase the risk of NEC in VLBW infants. The early prevention and treatment of anemia, strict evaluation of the indications for transfusion and enhanced monitoring after transfusion is encouraged in the NICU.
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| 10. |
- Wang, Jue
(författare)
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Regulation and polymorphism of CYP2A6, CYP2B6 and CYP2E1 : functional and clinical aspects
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cytochrome P450s constitute a superfamily of heme-binding monooxygenases that play important roles in the metabolism of endogenous substrates and a wide variety of exogenous substances, such as toxins and drugs, and participate as well in the biosynthesis of steroids, fatty acids, vitamins and bile acids. The P450s genes are subjects for large inter-individual variability in expression, which subsequently cause inter-individual differences in drug metabolism. A significant amount of the inter-individual variation can be attributed to genetic polymorphisms of P450 genes. The gene regulation of P450 expression occurs at multiple levels, e.g. transcription, RNA processing, translation and post-translation. Novel functional polymorphisms altering P450 expression were here identified in CYP2B6 and CYP2A6 genes. A novel CYP2B6*16 allele was found to carry two SNPs, 983T>C and 785A>G, and was present in 5 subjects having high plasma concentrations of efavirenz, all of African origin. This allele was found to significantly impair the expression level of CYP2B6, especially at the protein level, indicating impaired post-translational processing. Examination of the flanking regions of CYP2A6 gene revealed two functionally polymorphic elements. A strong enhancer was identified between -1005 and -1019, containing a SNP, -1013A>G. A known polymorphism in the 3´-UTR, CYP2A6*1B characterized by the gene conversion with CYP2A7 3´-UTR, was shown to be related to increased mRNA and protein levels and catalytic activity of coumarin. In vitro transfection experiments indicated that the stabilization of the CYP2A6*1B mRNA resulted in higher protein expression and also a higher rate of nicotine metabolism in vivo as shown by others. IL4 transcriptionally activates the expression of CYP2E1 gene, which is an important mechanism in P450 regulation by inflammation and infection. The regulation was shown to be mediated by two independent signaling pathways, the JAK-STAT6 and IRS1/2 pathways. These two pathways activate specific cis- and trans-acting elements, indicating the significance of the regulation. IL4-activated signaling and the possible feedback mechanisms revealed the complexity of P450 gene regulation. In summary, our studies contribute to the understanding of the regulatory mechanisms underlying the variable expression of P450 genes. Genetic polymorphisms contribute to a large extent of the variability, via multiple mechanisms. We have also shown that the regulation of CYP2E1 is mediated by a complex intracellular network.
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