Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii

ABSTRACT Caldicellulosiruptor bescii is the most thermophilic cellulose degrader known and is of great interest because of its ability to degrade nonpretreated plant biomass. For biotechnological applications, an efficient genetic system is required to engineer it to convert plant biomass into desired products. To date, two different genetically tractable lineages of C. bescii strains have been generated. The first (JWCB005) is based on a random deletion within the pyrimidine biosynthesis genes pyrFA, and the second (MACB1018) is based on the targeted deletion of pyrE, making use of a kanamycin resistance marker. Importantly, an active insertion element, ISCbe4, was discovered in C. bescii when it disrupted the gene for lactate dehydrogenase (ldh) in strain JWCB018, constructed in the JWCB005 background. Additional instances of ISCbe4 movement in other strains of this lineage are presented herein. These observations raise concerns about the genetic stability of such strains and their use as metabolic engineering platforms. In order to investigate genome stability in engineered strains of C. bescii from the two lineages, genome sequencing and Southern blot analyses were performed. The evidence presented shows a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and ISCbe4 elements within the genome of JWCB005, leading to massive genome rearrangements in its daughter strain, JWCB018. Such dramatic effects were not evident in the newer MACB1018 lineage, indicating that JWCB005 and its daughter strains are not suitable for metabolic engineering purposes in C. bescii. Furthermore, a facile approach for assessing genomic stability in C. bescii has been established. IMPORTANCE Caldicellulosiruptor bescii is a cellulolytic extremely thermophilic bacterium of great interest for metabolic engineering efforts geared toward lignocellulosic biofuel and bio-based chemical production. Genetic technology in C. bescii has led to the development of two uracil auxotrophic genetic background strains for metabolic engineering. We show that strains derived from the genetic background containing a random deletion in uracil biosynthesis genes (pyrFA) have a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and ISCbe4 insertion elements in their genomes compared to the wild type. At least one daughter strain of this lineage also contains large-scale genome rearrangements that are flanked by these ISCbe4 elements. In contrast, strains developed from the second background strain developed using a targeted deletion strategy of the uracil biosynthetic gene pyrE have a stable genome structure, making them preferable for future metabolic engineering studies.
Back from the edge of existence: A critical anthropology of trauma

How do local responses to trauma articulate with understandings of subjectivity, personhood, and meaning making? What therapeutic mechanisms seem to be at play? And how can the analytic lenses of anthropology help us understand—and maybe even facilitate—processes of recovery? In engaging these questions, the papers in this Special Issue lay the groundwork for what we might call a critical anthropology of trauma that bridges the divide between micro-level and macrolevel analyses of radical ruptures from the everyday. As several of the authors note, what we now call trauma is hardly a new topic for anthropologists, who have long paid special attention to events that push people to the very edges of their own existence, as well as the various ways they find their way back, often radically transformed (e.g., Crapanzano, 1985; LeviStrauss, 1963; Obeyesekere, 1984; Rosaldo, 1989; Spiro, 1987; Turner 1967). Such edge-of-existence experiences hinge on what Scarry (1985) calls the unmaking and remaking of worlds. Pushed to the very precipice of physical and/or psychological annihilation, the bonds that tether a person to the everyday world become stretched, distorted, and even torn; sometimes irreparably so. Such a state of ontological alienation is profoundly distressing. To regain their footing, people often turn to culturally available practices, symbols, and structures to help reorient them to the world. Anthropologists have used exegeses of such processes as the foundation for theories of the work of culture (Obeyesekere, 1990). By the mid-1990s, anthropological engagements with such edge-of-existence experiences had turned away from questions of psychological process and towards an examination of the social life of the category of such experiences; “trauma” as a cultural construct becamemarked as a distinct object of study (Young, 1995). Works in this vein are less concerned with underlying psychological mechanisms of trauma as with the social and cultural processes through which some experiences are recognized as “traumatic” and others are not, what this reveals about local understandings of moral responsibility, and the pathways by which recovery is imagined.
A UPnP Service to Control and Manage IEEE 1451 Transducers in Control Networks

This paper describes a new universal plug-and-play (UPnP) device, i.e., the Sensor Manager (SM), and its associated network service to access and control smart transducer networks based on the IEEE 1451 standard. In terms of the IEEE 1451, the SM shall be described as a network-capable application processor (NCAP) enhanced with features of the UPnP protocol, e.g., autodiscovery, autoconfiguration, and dynamic adaptation. The SM allows a control station located on the same control network to automatically detect any change in the sensor network. Moreover, the SM provides a general-purpose data-streaming mechanism based on the general event notification architecture and is fully UPnP compliant. The SM is presented as an element within an architecture where advanced features such as transmission modes can be configured. The model throughput is also discussed based on experimental results.
The Improvement of Nutritional Support with Percutaneous Endoscopic Gastrostomy

장기간 인공영양이 필요하며, 장관영양법이 정맥영양법보다 생리적이 Background/Aims: Percutaneous endoscopic gastrostomy (PEG) is the most common method of enteral nutrition for patients who require long term artificial nutrition. PEG has been used as a method of nutritional support; however, improvement of nutritional support via PEG has not yet been reported. In this study, we analyzed the efficacy of nutritional support via PEG. Methods: We conducted a retrospective analysis of 196 consecutive patients who underwent PEG at Kyung Hee University Hospital in Gang Dong from 2006 to 2012. We analyzed clinical characteristics, the method of nutritional support, and the proportion of intake to establish recommendations for nutritional requirements and the duration needed to reach the level of appropriate nutrition. Results: A total of 196 patients included 130 men and 66 women, and their mean age (standard deviation) was 69.1±14.0 years. Compared with caloric and protein supplementation before PEG, 113 kcal (13.8% of baseline) and 4.8 g of protein (17.5% of baseline) could be additionally supplied with PEG (P=0.001, respectively). The number of patients who could take more than 90% of the recommended requirements of caloric and protein supplementation after PEG showed increased caloric and protein intake by 25.4% and 20.2%, respectively, in comparison with those before PEG (P=0.001 and P=0.001, respectively). The mean duration of catch-up for more than 90% of the recommended caloric and protein intake was approximately 11 days. Procedure related complications and early mortality were reported in 8.1% and 0% of patients, respectively. Conclusions: PEG is an effective and safe nutritional support method for patients who require long term artificial nutrition. (Intest Res 2013;11:120-126)
Influence of Adhesion and Bacteriocin Production by Lactobacillus salivarius on the Intestinal Epithelial Cell Transcriptional Response

ABSTRACT Lactobacillus salivarius strain UCC118 is a human intestinal isolate that has been extensively studied for its potential probiotic effects in human and animal models. The objective of this study was to determine the effect of L. salivarius UCC118 on gene expression responses in the Caco-2 cell line to improve understanding of how the strain might modulate intestinal epithelial cell phenotypes. Exposure of Caco-2 cells to UCC118 led to the induction of several human genes (TNFAIP3, NFKBIA, and BIRC3) that are negative regulators of inflammatory signaling pathways. Induction of chemokines (CCL20, CXCL-1, and CXCL-2) with antimicrobial functions was also observed. Disruption of the UCC118 sortase gene srtA causes reduced bacterial adhesion to epithelial cells. Transcription of three mucin genes was reduced significantly when Caco-2 cells were stimulated with the ΔsrtA derivative of UCC118 compared to cells stimulated with the wild type, but there was no significant change in the transcription levels of the anti-inflammatory genes. UCC118 genes that were significantly upregulated upon exposure to Caco-2 cells were identified by bacterial genome microarray and consisted primarily of two groups of genes connected with purine metabolism and the operon for synthesis of the Abp118 bacteriocin. Following incubation with Caco-2 cells, the bacteriocin synthesis genes were transcribed at higher levels in the wild type than in the ΔsrtA derivative. These data indicate that L. salivarius UCC118 influences epithelial cells both through modulation of the inflammatory response and by modulation of intestinal cell mucin production. Sortase-anchored cell surface proteins of L. salivarius UCC118 have a central role in promoting the interaction between the bacterium and epithelial cells.
Special competencies for psychological assessment of torture survivors

In spite of the absolute prohibition against torture in international law, this grave human rights abuse is still practiced systematically and with impunity in the majority of countries around the world. Mental health professionals can play a positive role in the fight against torture and impunity, by developing competencies to assess the psychological sequelae of torture. High-quality psychological evidence can help to substantiate allegations of torture, thereby increasing the likelihood of success in civil, administrative, and criminal proceedings. This article will orient mental health professionals to issues specific to forensic assessment of torture survivors. It provides a brief introduction to the sociopolitical context of torture, reviews literature on the psychological sequelae of torture, introduces the reader to key competencies, offers information on strategies for producing documentary evidence and expert opinion, highlights ethical considerations, and suggests areas for development in the field.
“Our lifestyle is a mix-match”: Traditional healers talk about suicide and suicide prevention in South Africa

Practitioners of traditional African medicine (traditional healers) are an important part of the health care system in South Africa, yet their voices are often absent from discussions about public health. In this context, we set out to investigate how a group of traditional healers in South Africa understand suicide and suicide prevention. In-depth, semistructured interviews were conducted with 6 traditional healers and analysed using thematic content analysis. The traditional healers report they are frequently consulted by suicidal individuals and they are confident about their ability to help people in a suicidal crisis. Findings suggest that traditional healers understand suicidal behaviour as a symptom of social disconnection and cultural discontinuity. Traditional healers report that suicidal individuals can be helped by reestablishing interpersonal connections, reconnecting to family and ancestors, and renewing their cultural identities through rituals. These findings suggest that there is some congruence between the way traditional healers understand suicide and the Western scientific and biomedical literature. Our findings raise important questions about cultural approaches to suicide research which are commonly premised on dualistic thinking that constructs culture as something distinct from Western biomedicine.
Cicatricial alopecia as a sequel to furuncular myiasis of the scalp in an immunocompetent child

Furuncular myiasis (FM) is a type of cutaneous myiasis, a human infestation by maggots of Diptera flies. Our patient presented with scalp lesions closely mimicking pyoderma of the scalp, only to reveal crawling larvae of Lucilia sericata. Though the patient was promptly managed, cicatricial alopecia as a tell-tale sign of FM remained.
Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

ABSTRACT Pyrosequencing-based 16S rRNA gene surveys are increasingly utilized to study highly diverse bacterial communities, with special emphasis on utilizing the large number of sequences obtained (tens to hundreds of thousands) for species richness estimation. However, it is not yet clear how the number of operational taxonomic units (OTUs) and, hence, species richness estimates determined using shorter fragments at different taxonomic cutoffs correlates with the number of OTUs assigned using longer, nearly complete 16S rRNA gene fragments. We constructed a 16S rRNA clone library from an undisturbed tallgrass prairie soil (1,132 clones) and used it to compare species richness estimates obtained using eight pyrosequencing candidate fragments (99 to 361 bp in length) and the nearly full-length fragment. Fragments encompassing the V1 and V2 (V1+V2) region and the V6 region (generated using primer pairs 8F-338R and 967F-1046R) overestimated species richness; fragments encompassing the V3, V7, and V7+V8 hypervariable regions (generated using primer pairs 338F-530R, 1046F-1220R, and 1046F-1392R) underestimated species richness; and fragments encompassing the V4, V5+V6, and V6+V7 regions (generated using primer pairs 530F-805R, 805F-1046R, and 967F-1220R) provided estimates comparable to those obtained with the nearly full-length fragment. These patterns were observed regardless of the alignment method utilized or the parameter used to gauge comparative levels of species richness (number of OTUs observed, slope of scatter plots of pairwise distance values for short and nearly complete fragments, and nonparametric and parametric species richness estimates). Similar results were obtained when analyzing three other datasets derived from soil, adult Zebrafish gut, and basaltic formations in the East Pacific Rise. Regression analysis indicated that these observed discrepancies in species richness estimates within various regions could readily be explained by the proportions of hypervariable, variable, and conserved base pairs within an examined fragment.
Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of Saccharomyces cerevisiae

ABSTRACT Laboratory strains of Saccharomyces cerevisiae have been widely used as a model for studying eukaryotic cells and mapping the molecular mechanisms of many different human diseases. Industrial wine yeasts, on the other hand, have been selected on the basis of their adaptation to stringent environmental conditions and the organoleptic properties that they confer to wine. Here, we used a two-factor design to study the responses of a standard laboratory strain, CEN.PK113-7D, and an industrial wine yeast strain, EC1118, to growth temperatures of 15°C and 30°C in nitrogen-limited, anaerobic, steady-state chemostat cultures. Physiological characterization revealed that the growth temperature strongly impacted the biomass yield of both strains. Moreover, we found that the wine yeast was better adapted to mobilizing resources for biomass production and that the laboratory yeast exhibited higher fermentation rates. To elucidate mechanistic differences controlling the growth temperature response and underlying adaptive mechanisms between the strains, DNA microarrays and targeted metabolome analysis were used. We identified 1,007 temperature-dependent genes and 473 strain-dependent genes. The transcriptional response was used to identify highly correlated gene expression subnetworks within yeast metabolism. We showed that temperature differences most strongly affect nitrogen metabolism and the heat shock response. A lack of stress response element-mediated gene induction, coupled with reduced trehalose levels, indicated that there was a decreased general stress response at 15°C compared to that at 30°C. Differential responses among strains were centered on sugar uptake, nitrogen metabolism, and expression of genes related to organoleptic properties. Our study provides global insight into how growth temperature affects differential physiological and transcriptional responses in laboratory and wine strains of S. cerevisiae.
Evaluation of a Low-Cost Electrostatic Dust Fall Collector for Indoor Air Endotoxin Exposure Assessment

ABSTRACT Exposure to endotoxin in home environments has become a key issue in asthma and allergy research. Most studies have analyzed floor or mattress dust endotoxin, but its validity as a proxy for airborne exposure is unknown, while active airborne dust sampling is not feasible in large-scale population studies because of logistic and financial limitations. We therefore developed and evaluated a simple passive airborne dust collection method for airborne endotoxin exposure assessment. We explored an electrostatic dust fall collector (EDC), consisting of a 42- by 29.6-cm-sized folder with four electrostatic cloths exposed to the air. The EDC was tested during two 14-day periods in seven nonfarm and nine farm homes and in farm stables. In parallel, active airborne dust sampling was performed with Harvard impactors and floor dust collected by vacuuming, using nylon sampling socks. The endotoxin levels could be measured in all EDC cloth extracts. The levels (in EU/m2) between EDCs used simultaneously or in different sampling periods in the same home correlated strongly (r > 0.8). EDC endotoxin also correlated moderately to strongly (r = 0.6 to 0.8) with the endotoxin measured by active airborne dust sampling and living room floor dust sampling and—in farm homes—with the endotoxin captured by the EDC in stables. In contrast, endotoxin levels measured by floor dust sampling showed only a poor correlation with the levels measured by active airborne dust sampling. We therefore conclude that measuring endotoxin levels with the EDC is a valid measure of average airborne endotoxin exposure, while reproducibility over time is at least equivalent to that of reservoir dust analyses.
Optimal Post-Training Abstinence for Maximal Strength Expression

Tapering commonly precedes strength/power competitions to augment performance, and training abstinence is an extreme manifestation of taper. This study compared the effects of different training-abstinence intervals on several indices of strength. Postresting strength performance was compared in 54 young men who had abstained from a standardized weight training program for either 2, 3, 4, or 5 days. Testing included 1RM heel raise strength and isokinetic plantar flexion peak torque at 1.05 and 3.14 rad · s-1. Heel raise strength was greater at 4 days as compared to 2 or 5 days, whereas performance at 3 days was no different (p > .05) than any of the other rest intervals. Isokinetic plantar flexion peak torque at both 1.05 and 3.14 rad · s-1 was unaffected by any of the rest intervals. Small to moderate effect sizes were found for heel raise strength for groups resting 3 and 4 days as well as for slow and fast isokinetic peak torque for the group resting 4 days. It was concluded that a transient elevation in heel raise strength in young men appears to occur by the fourth day of abstinence from heavy-resistance heel-raise training. Under the same experimental conditions, it appears that a modest increase in both slow and fast isokinetic plantar-flexion strength may also occur.
High-Resolution Analysis of Gut Environment and Bacterial Microbiota Reveals Functional Compartmentation of the Gut in Wood-Feeding Higher Termites (Nasutitermes spp.)

ABSTRACT Higher termites are characterized by a purely prokaryotic gut microbiota and an increased compartmentation of their intestinal tract. In soil-feeding species, each gut compartment has different physicochemical conditions and is colonized by a specific microbial community. Although considerable information has accumulated also for wood-feeding species of the genus Nasutitermes, including cellulase activities and metagenomic data, a comprehensive study linking physicochemical gut conditions with the structure of the microbial communities in the different gut compartments is lacking. In this study, we measured high-resolution profiles of H2, O2, pH, and redox potential in the gut of Nasutitermes corniger termites, determined the fermentation products accumulating in the individual gut compartments, and analyzed the bacterial communities in detail by pyrotag sequencing of the V3-V4 region of the 16S rRNA genes. The dilated hindgut paunch (P3 compartment) was the only anoxic gut region, showed the highest density of bacteria, and accumulated H2 to high partial pressures (up to 12 kPa). Molecular hydrogen is apparently produced by a dense community of Spirochaetes and Fibrobacteres, which also dominate the gut of other Nasutitermes species. All other compartments, such as the alkaline P1 compartment (average pH, 10.0), showed high redox potentials and comprised small but distinct populations characteristic for each gut region. In the crop and the posterior hindgut compartments, the community was even more diverse than in the paunch. Similarities in the communities of the posterior hindgut and crop suggested that proctodeal trophallaxis or coprophagy also occurs in higher termites. The large sampling depths of pyrotag sequencing in combination with the determination of important physicochemical parameters allow cautious conclusions concerning the functions of particular bacterial lineages in the respective gut sections to be drawn.