Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characterization of 3-Methyl-4-nitrophenol Degradation in Burkholderia sp. Strain SJ98

Several strains have been reported to grow on 3-methyl-4-nitrophenol (3M4NP), the primary breakdown product of the excessively used insecticide fenitrothion. However, the microbial degradation of 3M4NP at molecular and biochemical levels remains unknown. Here, methyl-1,4-benzoquinone (MBQ) and methylhydroquinone (MHQ), rather than catechol proposed previously, were identified as the intermediates before ring cleavage during 3M4NP degradation by Burkholderia sp. strain SJ98. Real-time quantitative PCR analysis indicated that the pnpABA1CDEF cluster involved in para-nitrophenol (PNP) and 2-chloro-4-nitrophenol (2C4NP) catabolism was also likely responsible for 3M4NP degradation in this strain. Purified PNP 4-monooxygenase (PnpA) is able to catalyze the monooxygenation of 3M4NP to MBQ and exhibited an apparent Km value of 20.3 ± 2.54 μM for 3M4NP, and pnpA is absolutely necessary for the catabolism of 3M4NP by gene knock-out and complementation. PnpB, a 1,4-benzoquinone reductase catalyzes the reduction of MBQ to MHQ, and also found to enhance PnpA activity in vitro in the conversion of 3M4NP to MBQ. By sequential catalysis assays, PnpCD, PnpE, and PnpF were likely involved in the lower pathway of 3M4NP catabolism. Although NpcCD, NpcE, and NpcF are able to catalyze the sequential conversion of MHQ in vitro, these enzymes are unlikely involved in 3M4NP catabolism because their coding genes were not upregulated by 3M4NP induction in vivo. These results revealed that the enzymes involved in PNP and 2C4NP catabolism were also responsible for 3M4NP degradation in strain SJ98. This fills a gap in our understanding of the microbial degradation of 3M4NP at molecular and biochemical levels and also provides another example to illustrate the adaptive flexibility in microbial catabolism for structurally similar compounds.
Lethal and sublethal effects of atrazine, carbaryl, endosulfan, and octylphenol on the streamside salamander (Ambystoma barbouri)

Aricultural contaminants may be contributing to worldwide amphibian declines, but little is known about which agrichemicals pose the greatest threat to particular species. One reason for this is that tests of multiple contaminants under ecologically relevant conditions are rarely conducted concurrently. In this study, we examined the effects of 37‐d exposure to the agrichemicals atrazine (4, 40, and 400 μg/L), carbaryl (0.5, 5, and 50 μg/L), endosulfan (0.1, 1, and 10 μg/L for 31 d and 0.1, 10, and 100 μg/L for the last 6 d), and octylphenol (5, 50, and 500 μg/L) and to a solvent control on streamside salamanders (Ambystoma barbouri) in the presence and absence of food. We found that none of the agrichemicals significantly affected embryo survival, but that hatching was delayed by the highest concentration of octylphenol. In contrast to embryos, larval survival was reduced by the highest concentrations of carbaryl, endosulfan, and octylphenol. Growth rates were lower in the highest concentrations of endosulfan and octylphenol than in all other treatments, and the highest concentration of endosulfan caused respiratory distress. Significantly more carbaryl, endosulfan, and octylphenol tanks had larvae with limb deformities than did control tanks. Refuge use was independent of chemical exposure, but 10 μg/L of endosulfan and 500 μg/L of octylphenol decreased larval activity. Systematically tapping tanks caused a greater activity increase in larvae exposed to 400 μg/L of atrazine and 10 μg/L of endosulfan relative to solvent controls, suggesting underlying nervous system malfunction. Hunger stimulated a decrease in refuge use and an increase in activity, but this response was least pronounced in larvae exposed to the highest concentration of any of the four agrichemicals, possibly because these larvae were the most lethargic. More studies are needed that concurrently examine the effect of multiple contaminants on amphibians so we can better identify effective mitigating measures.
Weaving dreamcatchers: mothering among American Indian women who were teen mothers.

AIMS The aim of this study was to explore the mothering experience and practice among reservation-based adult American Indian women who had been adolescent mothers. BACKGROUND Adolescent American Indian women are at an elevated risk for teen pregnancy and poor maternal/child outcomes. Identifying mothering practices among this population may help guide intervention development that will improve health outcomes. DESIGN A collaborative orientation to community-based participatory research approach. METHODS Employing interpretive phenomenology, 30 adult American Indian women who resided on a Northwestern reservation were recruited. In-depth, face-to-face and telephone interviews were conducted between 2007-2008. FINDINGS Women shared their mothering experience and practice, which encompassed a lifespan perspective grounded in their American Indian cultural tradition. Four themes were identified as follows: mother hen, interrupted mothering and second chances, breaking cycles and mothering a community. Mothering originated in childhood, extended across their lifespan and moved beyond mothering their biological offspring. CONCLUSION These findings challenge the Western construct of mothering and charge nurses to seek culturally sensitive interventions that reinforce positive mothering practices and identify when additional mothering support is needed across a woman's lifespan.
SmartLeg: An intelligent active robotic prosthesis for lower-limb amputees

In recent years, there has been a worldwide interest in improvement of mobility of people with lower limb amputation. In spite of significant development of new technologies during the last decade, commercial below-knee and above-knee prostheses are still energetically passive devices. However, many locomotive functions, like walking up stairs and slopes, need significant power in knee and ankle joints. The additional power for doing previously mentioned activities needs to be achieved by means of external energy sources, which should be integral prosthetic components. This paper presents preliminary investigations towards an active robotic prosthesis that could potentially enable people with an above- or below-knee amputation to perform different types of motions that require power in lower limb joints. Our initial prototype, SmartLeg, integrates advanced prosthetic and robotic technology with the state-of-the-art machine learning algorithms capable of adapting the working of the prosthesis to the optimal gait and power consumption patterns, and which therefore provide means to customize the device to a particular user.
A Classification of Object-Relational Impedance Mismatch

Object and relational technologies are grounded in different paradigms. Each technology mandates that those who use it take a particular view of a universe of discourse. Incompatibilities between these views manifest as problems of an object-relational impedance mismatch. In this paper we propose a conceptual framework for the problem space of object-relational impedance mismatch and consequently distinguish four kinds of impedance mismatch. We show that each kind of impedance mismatch needs to be addressed using a different object-relational mapping strategy. Our framework provides a mechanism to explore issues of fidelity, integrity and completeness in the design and implementation of existing and new strategy choices. Our framework will be of benefit to standards bodies, tool vendors, designers and programmers as it will provide them with new insights into how to address problems of an object-relational impedance mismatch both at the most appropriate levels of abstraction and in the most appropriate way.
Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall.
Signaling Pathways Mediating the Induction of Apple Fruitlet Abscission1[C][W][OA]

Apple (Malus × domestica) represents an interesting model tree crop for studying fruit abscission. The physiological fruitlet drop occurring in this species can be easily magnified by using thinning chemicals, such as benzyladenine (BA), to obtain fruits with improved quality and marketability. Despite the economic importance of this process, the molecular determinants of apple fruitlet abscission are still unknown. In this research, BA was used to obtain fruitlet populations with different abscission potentials to be analyzed by means of a newly released 30K oligonucleotide microarray. RNAs were extracted from cortex and seed of apple fruitlets sampled over a 4-d time course, during which BA triggers fruit drop, and used for microarray hybridization. Transcriptomic profiles of persisting and abscising fruitlets were tested for statistical association with abscission potential, allowing us to identify molecular signatures strictly related to fruit destiny. A hypothetical model for apple fruitlet abscission was obtained by putting together available transcriptomic and metabolomic data. According to this model, BA treatment would establish a nutritional stress within the tree that is primarily perceived by the fruitlet cortex whose growth is blocked by resembling the ovary growth inhibition found in other species. In weaker fruits, this stress is soon visible also at the seed level, likely transduced via reactive oxygen species/sugar and hormones signaling cross talk, and followed by a block of embryogenesis and the consequent activation of the abscission zone.
A Discriminative Kernel-based Model to Rank Images from Text Queries

This paper introduces a discriminative model for the retrieval of images from text queries. Our approach formalizes the retrieval task as a ranking problem, and introduces a learning procedure optimizing a criterion related to the ranking performance. The proposed model hence addresses the retrieval problem directly and does not rely on an intermediate image annotation task, which contrasts with previous research. Moreover, our learning procedure builds upon recent work on the online learning of kernel-based classifiers. This yields an efficient, scalable algorithm, which can benefit from recent kernels developed for image comparison. The experiments performed over stock photography data show the advantage of our discriminative ranking approach over state-of-the-art alternatives (e.g. our model yields 26.3% average precision over the Corel dataset, which should be compared to 22.0%, for the best alternative model evaluated). Further analysis of the results shows that our model is especially advantageous over difficult queries such as queries with few relevant pictures or multiple-word queries.
Pharmacokinetic and Pharmacodynamic Evaluation of Liposomal Amikacin for Inhalation in Cystic Fibrosis Patients with Chronic Pseudomonal Infection

ABSTRACT The pharmacokinetics and pharmacodynamics of a novel liposomal amikacin for inhalation were evaluated in cystic fibrosis patients with chronic pseudomonas infection. Twenty-four patients from two studies received 500 mg of liposomal amikacin by inhalation once daily for 14 days. Serum, sputum, and 24-h urine samples were collected on days 1 and 14 of therapy; pulmonary function tests (PFT) and sputum for quantitative microbiology were assessed at baseline and serially for 14 days. Relationships between amikacin exposure in serum and sputum and absolute change in PFT endpoints and log10 CFU of Pseudomonas aeruginosa from baseline on days 7 and 14 of therapy were assessed. On days 7 and 14, absolute change from baseline in forced expiratory volume in 1 s (FEV1), percent predicted forced expiratory volume in 1 s (FEV1 % predicted), and forced expiratory flow between 25 and 75% of forced vital capacity (FEF25-75%) increased by 0.24 (P = 0.002) and 0.13 (P = 0.10) liters, 7.49 (P < 0.001) and 4.38 (P = 0.03), and 0.49 (P < 0.001) and 0.42 (P = 0.02) liters/s, respectively. In addition, relative change from baseline in FEV1 % predicted was 10.8% (P < 0.001) and 5.62% (P = 0.073) on days 7 and 14, respectively. While significant relationships between absolute change in PFT endpoints and the ratio of serum or sputum area under the concentration-time curve to the MIC (AUC/MIC) were not observed, relationships between change in log10 CFU and serum AUC/MIC ratio and change in log10 CFU and absolute changes in all PFT endpoints were significant. Together, these findings likely represent drug effect and warrant the further development of liposomal amikacin for inhalation.
Clinical evaluation of a biphasic calcium phosphate grafting material in the treatment of human periodontal intrabony defects

Purpose The aim of this study was to compare the clinical outcome of open flap debridement (OFD) with a biphasic calcium phosphate (BCP) graft to that of OFD without BCP graft for the treatment of intrabony periodontal defects (IBDs). Methods The study included 25 subjects that had at least one intrabony defect of 2- or 3-wall morphology and an intrabony component≥4 mm as detected radiographically. Subjects were randomly assigned to treatment with (BCP group, n=14) or without BCP (OFD group, n=11). Clinical parameters were recorded at baseline and 6 months after surgery and included the plaque index, gingival index, probing depth (PD), clinical attachment level (CAL), and gingival recession (REC). A stringent plaque control regimen was enforced for all of the patients during the 6-month observation period. Results In all of the treatment groups, significant PD reductions and CAL gains occurred during the study period (P<0.01). At 6 months, patients in the BCP group exhibited a mean PD reduction of 3.7±1.2 mm and a mean CAL gain of 3.0±1.1 mm compared to the baseline. Corresponding values for the patients treated with OFD were 2.5±0.8 mm and 1.4±1.0 mm, respectively. Compared to OFD group, the additional CAL gain was significantly greater in the patients in BCP group (P=0.028). The additional PD reduction was significant for the BCP group (P=0.048). The REC showed a significant increase in both groups, and the amount of recession was significantly smaller in the BCP group than OFD group (P=0.023). In radiographic evaluation, the height of the bone fill in the BCP group was significantly greater than OFD group. Conclusions The clinical benefits of BCP found in this study indicate that BCP may be an appropriate alternative to conventional graft materials.
Measuring the Mechanical Properties of Thin Metal Films by Means of Bulge Testing of Micromachined Windows

Free-standing films of gold and aluminum have been fabricated using standard micro-machining techniques. LPCVD silicon nitride films are deposited onto (100) silicon wafers. Square and rectangular silicon nitride membranes are made by anisotropic etching of the silicon substrates. Then, metal films are deposited onto the silicon nitride membranes by means of evaporation. Finally, the sacrificial silicon nitride film is etched away by means of reactive plasma etching, resulting in well-defined, square and rectangular metal membranes. Bulge testing of square windows allows one to determine the biaxial modulus of the film as well as the residual stress in it. Testing rectangular windows yields the plane-strain elastic modulus and the residual stress. Since deformation in rectangular membranes approaches plane-strain deformation, this geometry is ideal for studying the plastic properties of the metal films. Stress-strain curves can be readily determined from the load-deflection curves of rectangular membranes. The gold films have a biaxial modulus of 161±3 GPa and a plane-strain modulus of 105±5 GPa, slightly lower than the literature values for a (111) textured film. The yield stress of these films is approximately 231±17 MPa at 10 −4 % plastic strain. The elastic moduli of the aluminum films are 105±3 GPa and 76.4±0.7 GPa, respectively; the yield stress of these films is 187±30MPa.
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.
The placement of the head that maximizes predictability. An information theoretic approach

The minimization of the length of syntactic dependencies is a well-established principle of word order and the basis of a mathematical theory of word order. Here we complete that theory from the perspective of information theory, adding a competing word order principle: the maximization of predictability of a target element. These two principles are in conflict: to maximize the predictability of the head, the head should appear last, which maximizes the costs with respect to dependency length minimization. The implications of such a broad theoretical framework to understand the optimality, diversity and evolution of the six possible orderings of subject, object and verb are reviewed.
Trade, foreign inputs and firms' decisions: Theory and Evidence.

We investigate the effect of different channels through which input trade liberalization affects firms’ export decisions. We develop a trade model with heterogeneous firms and sectors of varying imported input intensity that reproduces different mechanisms through which the access to foreign inputs affects the performance of domestic firms. In industries with lower input tariffs (or more intensive in imported intermediate goods), more firms become exporters and export larger volumes. The effect of firm productivity on export status and export sales is greater for firms producing in these industries. The export selection process is reinforced by the access to foreign inputs. We provide strong empirical evidence in support of these theoretical predictions based on plant-level panel data from Argentina (1992-2001) and Chile (1990-1999). Our findings suggest that the impact of firm productivity on the probability of exporting and on the volume of exports is more pronounced for firms producing in industries that have a greater access to foreign inputs.
Ditto: a system for opportunistic caching in multi-hop wireless networks

This paper presents the design, implementation, and evaluation of Ditto, a system that opportunistically caches overheard data to improve subsequent transfer throughput in wireless mesh networks. While mesh networks have been proposed as a way to provide cheap, easily deployable Internet access, they must maintain high transfer throughput to be able to compete with other last-mile technologies. Unfortunately, doing so is difficult because multi-hop wireless transmissions interfere with each other, reducing the available capacity on the network. This problem is particularly severe in common gateway-based scenarios in which nearly all transmissions go through one or a few gateways from the mesh network to the Internet. Ditto exploits on-path as well as opportunistic caching based on overhearing to improve the throughput of data transfers and to reduce load on the gateways. It uses content-based naming to provide application independent caching at the granularity of small chunks, a feature that is key to being able to cache partially overheard data transfers. Our evaluation of Ditto shows that it can achieve significant performance gains for cached data, increasing throughput by up to 7x over simpler on-path caching schemes, and by up to an order of magnitude over no caching.
The susceptibility of two species of wallaby to infection with Trypanosoma evansi.

OBJECTIVE To determine the susceptibility of the agile wallaby (Macropus agilis) and the dusky pademelon (Thylogale brunil) to infection with Trypanosoma evansi. METHOD Two agile wallabies and three dusky pademelons were experimentally infected with between 5 x 10(4) and 10 x 10(4) T evansi from a cryopreserved stabilate isolated from an indonesian buffalo. Animals were observed twice daily for clinical signs and blood was collected every 3 days to determine parasitaemia. Necropsy was conducted on animals that died or were euthanised when in extremis and representative tissue sections examined. RESULTS All wallabies developed a high parasitaemia by 6 days after infection, which persisted until death or euthanasia in extremis, between days 8 and 61. Clinical signs included anorexia, weakness and ataxia. Anaemia occurred in one wallaby that survived for 61 days. Gross pathological changes varied between animals. They included pericarditis, serous atrophy of fat, splenomegaly, ulcerative gastritis and enteritis. Histological changes were characterised by a mononuclear cell infiltration of the connective tissue of most organs with little cellular destruction. Striking lesions were seen in the choroid, heart, stomach and small intestine. CONCLUSION Agile wallabies and pademelons are highly susceptible to infection with T evansi. Wallabies, therefore, have the potential to spread T evansi within New Guinea and Australia if infection is introduced. Mortality is likely to be high thereby acting as an indicator of recent introduction. Histological changes seen in wallabies infected with T evansi are diagnostic for infections occurring in Australia and Papua New Guinea.