6,851 research outputs found
Growth study on chrysene degraders isolated from polycyclic aromatic hydrocarbon polluted soils in Nigeria
Acinetobacter anitratus, Alcaligenes faecalis, Acinetobacter mallei and Micrococcus varians were isolated from polycyclic aromatic hydrocarbon polluted soils by enrichment culture using chrysene assole carbon and energy source. Physiochemical evaluation revealed that these isolates grew well at a temperature range of 20 - 40°C, pH 6.0-8.0 but less tolerable to various salt concentrations except Micrococcus varians which grew at 1.0 to 7.5% NaCl. These organisms utilized chrysene, anthracene, naphthalene, crude oil, kerosene, diesel and engine oil as sole carbon source. None could utilize benzene, hexane, xylene, phenol and toluene as carbon sources. Growth study of the isolates on 0.1%(w/v) chrysene resulted in highest cell density of 8.8x107, 7.9x107, 6.3x106, 6.3x106 cfu/ml for A. anitratus, Alc. faecalis, A. mallei and M. varians, respectively. There was statistical significant difference (P< 0.05) in the growth of these organisms on chrysene as sole carbon and energy source when compared with non-chrysene control. This study indicates the potential of these hitherto unreported tropical bacterial strains as chrysene degraders and their use in biodegradation processes involvingpetrochemical product
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Mobile phones and wrong numbers: how Maasai agro-pastoralists form and use accidental social ties in East Africa
Mobile phones are recognized as important new tools for rural development in the Global South, but few studies have
examined how phones can shape social networks. This study documents a new type of social tie, enabled by mobile phones, that to our
knowledge has not previously been discussed in academic literature. In 2018, we discovered that Maasai pastoralists in northern Tanzania
create new social ties through wrong numbers, a phenomenon with implications for theory on social networks and path dependency.
We used a mixed ethnographic and survey-based design to examine the following: (1) the conditions under which wrong number
connections (WNCs) are made; (2) the incidence of these connections in the study area; and (3) the association between WNCs and
multiple livelihood strategies. Working in 10 rural communities in Tanzania, we conducted 16 group interviews with men about their
phone use and found that WNCs are diverse and can provide households with important information, resources, and opportunities
from an expansive geographic area. (Nine separate interviews with groups of women revealed that women do not create WNCs.) Based
on early qualitative findings, we designed and conducted a standardized survey with 317 household heads. We found that 46% of
respondents have had WNCs. Furthermore, multivariate regression models show a significant association between WNCs and the
controversial practice of leasing land in one district. Taken together, our findings show that WNCs can be seen as innovations in social
networking that reduce path dependency, increase the range of potential outcomes, and hold important implications for rural livelihoods
in East Africa
A method for sensitivity analysis to assess the effects of measurement error in multiple exposure variables using external validation data
Measurement error in self-reported dietary intakes is known to bias the association between dietary intake and a health outcome of interest such as risk of a disease. The association can be distorted further by mismeasured confounders, leading to invalid results and conclusions. It is, however, difficult to adjust for the bias in the association when there is no internal validation data
Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding
In this study, we explore nucleation and the transition state ensemble of the
ribosomal protein S6 using a Monte Carlo Go model in conjunction with
restraints from experiment. The results are analyzed in the context of
extensive experimental and evolutionary data. The roles of individual residues
in the folding nucleus are identified and the order of events in the S6 folding
mechanism is explored in detail. Interpretation of our results agrees with, and
extends the utility of, experiments that shift f-values by modulating
denaturant concentration and presents strong evidence for the realism of the
mechanistic details in our Monte Carlo Go model and the structural
interpretation of experimental f-values. We also observe plasticity in the
contacts of the hydrophobic core that support the specific nucleus. For S6,
which binds to RNA and protein after folding, this plasticity may result from
the conformational flexibility required to achieve biological function. These
results present a theoretical and conceptual picture that is relevant in
understanding the mechanism of nucleation in protein folding.Comment: PNAS in pres
Simple models of protein folding and of non--conventional drug design
While all the information required for the folding of a protein is contained
in its amino acid sequence, one has not yet learned how to extract this
information to predict the three--dimensional, biologically active, native
conformation of a protein whose sequence is known. Using insight obtained from
simple model simulations of the folding of proteins, in particular of the fact
that this phenomenon is essentially controlled by conserved (native) contacts
among (few) strongly interacting ("hot"), as a rule hydrophobic, amino acids,
which also stabilize local elementary structures (LES, hidden, incipient
secondary structures like --helices and --sheets) formed early
in the folding process and leading to the postcritical folding nucleus (i.e.,
the minimum set of native contacts which bring the system pass beyond the
highest free--energy barrier found in the whole folding process) it is possible
to work out a succesful strategy for reading the native structure of designed
proteins from the knowledge of only their amino acid sequence and of the
contact energies among the amino acids. Because LES have undergone millions of
years of evolution to selectively dock to their complementary structures, small
peptides made out of the same amino acids as the LES are expected to
selectively attach to the newly expressed (unfolded) protein and inhibit its
folding, or to the native (fluctuating) native conformation and denaturate it.
These peptides, or their mimetic molecules, can thus be used as effective
non--conventional drugs to those already existing (and directed at neutralizing
the active site of enzymes), displaying the advantage of not suffering from the
uprise of resistance
Nucleation phenomena in protein folding: The modulating role of protein sequence
For the vast majority of naturally occurring, small, single domain proteins
folding is often described as a two-state process that lacks detectable
intermediates. This observation has often been rationalized on the basis of a
nucleation mechanism for protein folding whose basic premise is the idea that
after completion of a specific set of contacts forming the so-called folding
nucleus the native state is achieved promptly. Here we propose a methodology to
identify folding nuclei in small lattice polymers and apply it to the study of
protein molecules with chain length N=48. To investigate the extent to which
protein topology is a robust determinant of the nucleation mechanism we compare
the nucleation scenario of a native-centric model with that of a sequence
specific model sharing the same native fold. To evaluate the impact of the
sequence's finner details in the nucleation mechanism we consider the folding
of two non- homologous sequences. We conclude that in a sequence-specific model
the folding nucleus is, to some extent, formed by the most stable contacts in
the protein and that the less stable linkages in the folding nucleus are solely
determined by the fold's topology. We have also found that independently of
protein sequence the folding nucleus performs the same `topological' function.
This unifying feature of the nucleation mechanism results from the residues
forming the folding nucleus being distributed along the protein chain in a
similar and well-defined manner that is determined by the fold's topological
features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear
On the stability of renormalizable expansions in three-dimensional gravity
Preliminary investigations are made for the stability of the expansion
in three-dimensional gravity coupled to various matter fields, which are
power-counting renormalizable. For unitary matters, a tachyonic pole appears in
the spin-2 part of the leading graviton propagator, which implies the unstable
flat space-time, unless the higher-derivative terms are introduced. As another
possibility to avoid this spin-2 tachyon, we propose Einstein gravity coupled
to non-unitary matters. It turns out that a tachyon appears in the spin-0 or -1
part for any linear gauges in this case, but it can be removed if non-minimally
coupled scalars are included. We suggest an interesting model which may be
stable and possess an ultraviolet fixed point.Comment: 32 pages. (A further discussion to avoid tachyons is included. To be
Published in Physical Review D.
RNA secondary structure formation: a solvable model of heteropolymer folding
The statistical mechanics of heteropolymer structure formation is studied in
the context of RNA secondary structures. A designed RNA sequence biased
energetically towards a particular native structure (a hairpin) is used to
study the transition between the native and molten phase of the RNA as a
function of temperature. The transition is driven by a competition between the
energy gained from the polymer's overlap with the native structure and the
entropic gain of forming random contacts. A simplified Go-like model is
proposed and solved exactly. The predicted critical behavior is verified via
exact numerical enumeration of a large ensemble of similarly designed
sequences.Comment: 4 pages including 2 figure
The Atrial Fibrillation Risk Score for Hyperthyroidism Patients
Thyrotoxicosis (TT) is associated with an increase in both total and
cardiovascu-lar mortality. One of the main thyrotoxicosis risks is Atrial
Fibrillation (AF). Right AF predicts help medical personal prescribe the
correct medicaments and correct surgical or radioiodine therapy. The main goal
of this study is creating a method for practical treatment and diagnostic AF.
This study proposes a new method for assessing the risk of occurrence atrial
fibrillation for patients with TT. This method considers both the features of
the complication and the specifics of the chronic disease. A model is created
based on case histories of patients with thyrotoxicosis. We used Machine
Learning methods for creating several models. Each model has advantages and
disadvantages depending on the diagnostic and medical purposes. The resulting
models show high results in the different metrics of the prediction of AF.
These models interpreted and simple for use. Therefore, models can be used as
part of the support and decision-making system (DSS) by medical specialists in
the treatment and diagnostic of AF
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Research-based versus clinical serum creatinine measurements and the association of acute kidney injury with subsequent kidney function: findings from the Chronic Renal Insufficiency Cohort study.
Background:Observational studies relying on clinically obtained data have shown that acute kidney injury (AKI) is linked to accelerated chronic kidney disease (CKD) progression. However, prior reports lacked uniform collection of important confounders such as proteinuria and pre-AKI kidney function trajectory, and may be susceptible to ascertainment bias, as patients may be more likely to undergo kidney function testing after AKI. Methods:We studied 444 adults with CKD who participated in the prospective Chronic Renal Insufficiency Cohort (CRIC) Study and were concurrent members of a large integrated healthcare delivery system. We estimated glomerular filtration rate (eGFR) trajectories using serum creatinine measurements from (i) the CRIC research protocol (yearly) and (ii) routine clinical care. We used linear mixed effects models to evaluate the associations of AKI with acute absolute change in eGFR and post-AKI eGFR slope, and explored whether these varied by source of creatinine results. Models were adjusted for demographic characteristics, diabetes status and albuminuria. Results:During median follow-up of 8.5 years, mean rate of eGFR loss was -0.31 mL/min/1.73 m2/year overall, and 73 individuals experienced AKI (55% Stage 1). A significant interaction existed between AKI and source of serum creatinine for acute absolute change in eGFR level after discharge; in contrast, AKI was independently associated with a faster rate of eGFR decline (mean additional loss of -0.67 mL/min/1.73 m2/year), which was not impacted by source of serum creatinine. Conclusions:AKI is independently associated with subsequent steeper eGFR decline regardless of the serum creatinine source used, but the strength of association is smaller than observed in prior studies after taking into account key confounders such as pre-AKI eGFR slope and albuminuria
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