The ion-aerosol interactions from the ion mobility and aerosol particle size distribution measurements on January 17 and February 18, 2005 at Maitri, Antarctica - A case study

A case study for the ion–aerosol interactions is presented from the simultaneous measurements of mobility spectra of atmospheric ions in the mobility range of 2.29 to 2.98 × 10 − 4 cm2 V − 1 s −1 (diameter range 0.41–109 nm) and of size distribution of atmospheric aerosol particles in the size ranges of 4.4–700 nm and 500–20,000 nm diameters made at Maitri (70°45′52′ ′S, 11°44′2.7′ ′E; 130 m above mean sea level), Antarctica, on two days January 17 and February 18, 2005, with contrasting meteorological conditions. In contrast to January 17, on February 18, winds were stronger from the morning to noon and lower from the noon to evening, atmospheric pressure was lower, cloudiness was more, the land surface remained snow-covered after a blizzard on February 16 and 17 and the airmass over Maitri, descended from an altitude of ~3 km after an excursion over ocean. On these days mobility spectra showed two modes, corresponding to intermediate ions and light large ions and an indication of additional one/two maxima for small/cluster ions and heavy large ions. The small ions generated by cosmic rays, and the nucleation mode particles generated probably by photochemical reactions grew in size by condensation of volatile trace gases on them and produced the cluster and intermediate ion modes and the Aitken particle mode in ion/particle spectra. Particles in the size range of 9–26 nm have been estimated to grow at the rate of 1.9 nm h − 1 on February 18, 2005. Both, ions and aerosol particles show bimodal size distributions in the 16–107 nm size range, and comparison of the two size distributions suggests the formation of multiple charged ions. Attachment of small ions to particles in this bimodal distribution of Aitken particles together with the formation of multiple charged ions are proposed to result in the light and heavy large ion modes. Growth of the nucleation mode particles on February 18, 2005 is associated with the passage of the airmass over ocean. In contrast, though the ion size distributions were not much different, the aerosol size distributions did not show a dominant peak for the formation and growth of nucleation mode particles on January 17. More measurements are needed before the conclusion of this case study is generalized

The role of electron-electron scattering in spin transport

We investigate spin transport in quasi 2DEG formed by III-V semiconductor heterojunctions using the Monte Carlo method. The results obtained with and without electron-electron scattering are compared and appreciable difference between the two is found. The electron-electron scattering leads to suppression of Dyakonov-Perel mechanism (DP) and enhancement of Elliott-Yafet mechanism (EY). Finally, spin transport in InSb and GaAs heterostructures is investigated considering both DP and EY mechanisms. While DP mechanism dominates spin decoherence in GaAs, EY mechanism is found to dominate in high mobility InSb. Our simulations predict a lower spin relaxation/decoherence rate in wide gap semiconductors which is desirable for spin transport.Comment: to appear in Journal of Applied Physic

New insights into electron spin dynamics in the presence of correlated noise

The changes of the spin depolarization length in zinc-blende semiconductors when an external component of correlated noise is added to a static driving electric field are analyzed for different values of field strength, noise amplitude and correlation time. Electron dynamics is simulated by a Monte Carlo procedure which keeps into account all the possible scattering phenomena of the hot electrons in the medium and includes the evolution of spin polarization. Spin depolarization is studied by examinating the decay of the initial spin polarization of the conduction electrons through the D'yakonov-Perel process, the only relevant relaxation mechanism in III-V crystals. Our results show that, for electric field amplitude lower than the Gunn field, the dephasing length shortens with the increasing of the noise intensity. Moreover, a nonmonotonic behavior of spin depolarization length with the noise correlation time is found, characterized by a maximum variation for values of noise correlation time comparable with the dephasing time. Instead, in high field conditions, we find that, critically depending on the noise correlation time, external fluctuations can positively affect the relaxation length. The influence of the inclusion of the electron-electron scattering mechanism is also shown and discussed.Comment: Published on "Journal of Physics: Condensed Matter" as "Fast Track Communications", 11 pages, 9 figure

Size-distribution of submicron aerosol particles over the Indian Ocean during IFP-99 of INDOEX

Measurements of the size-distribution of submicron aerosol particles of diameter from 0.003 to 1 μm are made over the Indian Ocean during the IFP-99 of the Indian Ocean Experiment (INDOEX). Measurements are made during the onward journey from Goa to Port Louis, Mauritius from 20 January to 11 February 1999 onboard ORV Sagar Kanya and during the return journey from Port Louis to Male from 22 February to 1 March 1999 onboard Ronald H. Brown. Observations show large concentrations in the range of 2-6 × 103 particles/cm3 over the Indian Ocean in the northern hemisphere and these drop down to about 500 particles/cm3 in the southern hemisphere. However, the aerosol concentrations show a peak of about 3 × 103 particles/cm3 at 13°S. In the northern hemisphere, the concentration of particles of diameter < 0.0749 μm increases from 14°N to 1°N and then steeply falls. On the other hand, the concentration of particles of diameter > 0.0749 μm keeps decreasing up to 6°S. Size distributions of particles at open sea in the northern hemisphere show a maximum at 0.133 μm and minimum at 0.0422 μm and are generally openended at the smaller size end. The size-distributions of particles are sometimes relatively flat from 0.0133 to 0.237 μm when the particle concentrations are low in the southern hemisphere. The transport and accumulation of aerosol particles in the Inter-Tropical Convergence Zone is discussed. The relative abundance of large versus small particles is examined with respect to the variation of surface atmospheric pressure along the route

Chemoreflex Sensitization Occurs in Both Male and Female Rats During Recovery from Acute Lung Injury

Introduction: Sex-specific patterns in respiratory conditions, such as asthma, COPD, cystic fibrosis, obstructive sleep apnea, and idiopathic pulmonary fibrosis, have been previously documented. Animal models of acute lung injury (ALI) have offered insights into sex differences, with male mice exhibiting distinct lung edema and vascular leakage compared to female mice. Our lab has provided evidence that the chemoreflex is sensitized in male rats during the recovery from bleomycin-induced ALI, but whether sex-based chemoreflex changes occur post-ALI is not known. To bridge this gap, the current study employed the bleomycin-induced ALI animal model to investigate sex-based differences in chemoreflex activation during the recovery from ALI. Methods: ALI was induced using a single intra-tracheal instillation of bleomycin (bleo, 2.5 mg/Kg) (day 1). Resting respiratory frequency (fR) was measured at 1-2 days pre-bleo, day 7 (D7) post-bleo, and 1 month (1 mth) post-bleo. The chemoreflex responses to hypoxia (10% O2, 0% CO2) and normoxic-hypercapnia (21% O2, 5% CO2) were measured before bleo administration (pre-bleo) and 1 mth post-bleo using whole-body plethysmography. The apnea-hypopnea Index (AHI), post-sigh apneas, and sighs were measured at each time point. Results: There were no significant differences in resting fR between male and female rats at the pre-bleo time point or in the increase in resting fR at D7 post-bleo. At 1 mth post-bleo, the resting fR was partially restored in both sexes but the recovery towards normal ranges of resting fR was significantly lower in male rats. The AHI, post-sigh apneas, and sighs were not different between male and female rats pre-bleo and 1 mth post-bleo. However, at D7 post-bleo, the male rats exhibited a higher AHI than female rats. Both male and female rats exhibited a sensitized chemoreflex in response to hypoxia and normoxic-hypercapnia with no significant differences between sexes. Conclusion: A sex difference in resting ventilatory parameters occurs post ALI with a prolonged increase in resting fR and larger AHI in male rats. On the other hand, we did not find any sex differences in the chemoreflex sensitization that occurs at 1 mth post-bleo. This work contributes to a better understanding of sex-based variations in lung disorders

Time-Dependent Alteration in the Chemoreflex Post-Acute Lung Injury

Acute lung injury (ALI) induces inflammation that disrupts the normal alveolar-capillary endothelial barrier which impairs gas exchange to induce hypoxemia that reflexively increases respiration. The neural mechanisms underlying the respiratory dysfunction during ALI are not fully understood. The purpose of this study was to investigate the role of the chemoreflex in mediating abnormal ventilation during acute (early) and recovery (late) stages of ALI. We hypothesized that the increase in respiratory rate (fR) during post-ALI is mediated by a sensitized chemoreflex. ALI was induced in male Sprague-Dawley rats using a single intra-tracheal injection of bleomycin (Bleo: low-dose = 1.25 mg/Kg or high-dose = 2.5 mg/Kg) (day 1) and respiratory variables- fR, Vt (Tidal Volume), and VE (Minute Ventilation) in response to 10% hypoxia (10% O2, 0% CO2) and 5% hypercapnia/21% normoxia (21% O2, 5% CO2) were measured weekly from W0-W4 using whole-body plethysmography (WBP). Our data indicate sensitization (∆fR = 93 ± 31 bpm, p \u3c 0.0001) of the chemoreflex at W1 post-ALI in response to hypoxic/hypercapnic gas challenge in the low-dose bleo (moderate ALI) group and a blunted chemoreflex (∆fR = -0.97 ± 42 bpm, p \u3c 0.0001) at W1 post-ALI in the high-dose bleo (severe ALI) group. During recovery from ALI, at W3-W4, both low-dose and high-dose groups exhibited a sensitized chemoreflex in response to hypoxia and normoxic-hypercapnia. We then hypothesized that the blunted chemoreflex at W1 post-ALI in the high-dose bleo group could be due to near maximal tonic activation of chemoreceptors, called the ceiling effect . To test this possibility, 90% hyperoxia (90% O2, 0% CO2) was given to bleo treated rats to inhibit the chemoreflex. Our results showed no changes in fR, suggesting absence of the tonic chemoreflex activation in response to hypoxia at W1 post-ALI. These data suggest that during the acute stage of moderate (low-dose bleo) and severe (high-dose bleo) ALI, chemoreflex activity trends to be slightly sensitized and blunted, respectively while it becomes significantly sensitized during the recovery stage. Future studies are required to examine the molecular/cellular mechanisms underlying the time-course changes in chemoreflex sensitivity post-ALI

Effect of phyto additives and Saccharomyces cerevisiae on rumen ferementation and microbial profile in buffaloes

To study the effect of plants containing plant secondary metabolites (PSM) and Saccharomyces cerevisiae on rumen ferementation and microbial profile, four fistulated adult buffaloes were fed in 4×4 Latin square design. The four groups were, control, without additive; T1, mixture of harad seed pulp and garlic bulb (2% of DMI); T2, S. cerevisiae (350g feremented feed containing S. cerevisiae 106 /g); T3, mixture of harad seed pulp, garlic bulb and S. cerevisiae. All the animals were fed on a basal diet consisting of wheat straw and concentrate mixture in 50:50 ratio. Daily DM intake was similar in all the four groups. Feeding of any of the dietary treatments did not affect rumen fluid pH, concentration of ammonia N and lactic acid. The total volatile fatty acids and its fractions except butyrate were also not influenced by supplementation of any of the additives. The activities of ruminal enzymes viz. carboxymethylcellulase, xylanase, avicelase and acetyl esterase were similar in all the four groups. The rumen microbial density of total bacteria, Ruminococcus flavefaciences, R. albus, methanogens and fungi were not changed whereas Fibrobacter succinogenes and protozoa populations were significantly reduced in T1 but were at par of control by inclusion of yeast in the diet. It is concluded that mixture of harad and garlic alone or in combination with yeast culture did not influence rumen fermentation however microbial profile (F. succinogenes and protozoa) was improved by feeding yeast as additive. The additives tested seem to have potential to alter rumen microbial ecology and can further be explored for its efficacy in improving the performance of the animals

Third-generation RNA-sequencing analysis : graph alignment and transcript assembly with long reads

The information contained in the genome of an organism, its DNA, is expressed through transcription of its genes to RNA, in quantities determined by many internal and external factors. As such, studying the gene expression can give valuable information for e.g. clinical diagnostics. A common analysis workflow of RNA-sequencing (RNA-seq) data consists of mapping the sequencing reads to a reference genome, followed by the transcript assembly and quantification based on these alignments. The advent of second-generation sequencing revolutionized the field by reducing the sequencing costs by 50,000-fold. Now another revolution is imminent with the third-generation sequencing platforms producing an order of magnitude higher read lengths. However, higher error rate, higher cost and lower throughput compared to the second-generation sequencing bring their own challenges. To compensate for the low throughput and high cost, hybrid approaches using both short second-generation and long third-generation reads have gathered recent interest. The first part of this thesis focuses on the analysis of short-read RNA-seq data. As short-read mapping is an already well-researched field, we focus on giving a literature review of the topic. For transcript assembly we propose a novel (at the time of the publication) approach of using minimum-cost flows to solve the problem of covering a graph created from the read alignments with a set of paths with the minimum cost, under some cost model. Various network-flow-based solutions were proposed in parallel to, as well as after, ours. The second part, where the main contributions of this thesis lie, focuses on the analysis of long-read RNA-seq data. The driving point of our research has been the Minimum Path Cover with Subpath Constraints (MPC-SC) model, where transcript assembly is modeled as a minimum path cover problem, with the addition that each of the chains of exons (subpath constraints) created from the long reads must be completely contained in a solution path. In addition to implementing this concept, we experimentally studied different approaches on how to find the exon chains in practice. The evaluated approaches included aligning the long reads to a graph created from short read alignments instead of the reference genome, which led to our final contribution: extending a co-linear chaining algorithm from between two sequences to between a sequence and a directed acyclic graph.Transkriptiossa organismin geenien mallin mukaan luodaan RNA-molekyyleja. Lukuisat tekijät, sekä solun sisäiset että ulkoiset, määrittävät mitä geenejä transkriptoidaan, ja missä määrin. Tämän prosessin tutkiminen antaa arvokasta tietoa esimerkiksi lääketieteelliseen diagnostiikkaan. Yksi yleisistä RNA-sekvensointidatan analyysitavoista koostuu kolmesta osasta: lukujaksojen (read sequences) linjaus referenssigenomiin, transkriptien kokoaminen, ja transkriptien ekspressiotasojen määrittäminen. Toisen sukupolven sekvensointiteknologian kehityksen myötä sekvensoinnin hinta laski huomattavasti, mikä salli RNA-sekvensointidatan käytön yhä useampaan tarkoitukseen. Nyt kolmannen sukupolven sekvensointiteknologiat tarjoavat kertaluokkaa pidempiä lukujaksoja, mikä laajentaa analysointimahdollisuuksia. Kuitenkin suurempi virhemäärä, korkeampi hinta ja pienempi määrä tuotettua dataa tuovat omat haasteensa. Toisen ja kolmannen sukupolven teknologioiden käyttäminen yhdessä, ns. hybridilähestymistapa, on tutkimussuunta joka on kerännyt paljon kiinnostusta viimeaikoina. Tämän tutkielman ensimmäinen osa keskittyy toisen sukupolven, eli ns. lyhyiden RNA-lukujaksojen (short read), analyysiin. Näiden lyhyiden lukujaksojen linjausta referenssigenomiin on tutkittu jo 2000-luvulla, joten tällä alueella keskitymme olemassaolevaan kirjallisuuteen. Transkriptien kokoamisen alalta esittelemme metodin, joka käyttää vähimmäiskustannusvirtauksen (minimum-cost flow) mallia. Vähimmäiskustannusvirtauksen mallissa lukujaksoista luotu verkko peitetään joukolla polkuja, joiden kustannus on pienin mahdollinen. Virtausmalleja on käytetty myös muiden tutkijoiden kehittämissä analyysityökaluissa. Tämän tutkielman suurin kontribuutio on toisessa osassa, joka keskittyy ns. pitkien RNA-lukujaksojen (long read) analysointiin. Tutkimuksemme lähtökohtana on ollut malli, jossa pienimmän polkupeitteen (Minimum Path Cover) ongelmaan lisätään alipolkurajoitus (subpath constraint). Jokainen alipolkurajoitus vastaa eksoniketjua (exon chain), jotka jokin pitkä lukujakso peittää, ja jokaisen alipolkurajoituksen täytyy sisältyä kokonaan johonkin polkupeitteen polkuun. Tämän konseptin toteuttamisen lisäksi testasimme kokeellisesti erilaisia lähestymistapoja eksoniketjujen löytämiseksi. Näihin testattaviin lähestymistapoihin kuului pitkien lukujaksojen linjaaminen suoraan lyhyistä lukujaksoista luotuun verkkoon referenssigenomin sijaan. Tämä lähestymistapa johti tämän tutkielman viimeiseen kontribuutioon: kolineaarisen ketjun (co-linear chaining) algoritmin yleistäminen kahden sekvenssin sijasta sekvenssiin ja suunnattuun syklittömään verkkoon

Human marginal zone B cell development from early T2 progenitors

B cells emerge from the bone marrow as transitional (TS) B cells that differentiate through T1, T2, and T3 stages to become naive B cells. We have identified a bifurcation of human B cell maturation from the T1 stage forming IgMhi and IgMlo developmental trajectories. IgMhi T2 cells have higher expression of α4β7 integrin and lower expression of IL-4 receptor (IL4R) compared with the IgMlo branch and are selectively recruited into gut-associated lymphoid tissue. IgMhi T2 cells also share transcriptomic features with marginal zone B cells (MZBs). Lineage progression from T1 cells to MZBs via an IgMhi trajectory is identified by pseudotime analysis of scRNA-sequencing data. Reduced frequency of IgMhi gut-homing T2 cells is observed in severe SLE and is associated with reduction of MZBs and their putative IgMhi precursors. The collapse of the gut-associated MZB maturational axis in severe SLE affirms its existence in health.</p