Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and characterization of Tn5 insertion mutants of Erwinia chrysanthemi that are deficient in polygalacturonate catabolic enzymes oligogalacturonate lyase and 3-deoxy-D-glycero-2,5-hexodiulosonate dehydrogenase

Mutants of Erwinia chrysanthemi EC16 deficient in the polygalacturonate catabolic enzymes oligogalacturonate lyase (Ogl-) and 3-deoxy-D-glycero-2,5-hexodiulosonate (ketodeoxyuronate) dehydrogenase (KduD-) were obtained by Tn5 mutagenesis using the R plasmid pJB4JI. Ogl- Exu+ (Exu+, D-galacturonate utilization) and KduD- Exu- strains macerated potato tuber tissue and utilized glucose, glycerol, and gluconate, but they did not utilize polygalacturonate, unsaturated digalacturonate, or saturated digalacturonate. Genetic and physical evidence indicated that the Ogl- mutants and a KduD- recombinant contained a single copy of Tn5 and that Tn5 (Kmr) was linked to the mutant phenotypes. In the Ogl+ parents, basal levels of oligogalacturonate lyase were present in glycerol-grown cells and induced levels were present with saturated or unsaturated digalacturonate, while oligogalacturonate lyase was undetectable under similar conditions in Ogl- strains. Pectate lyase, polygalacturonase, and ketodeoxyuronate dehydrogenase were induced in an Ogl- strain by 3-deoxy-D-glycero-2,5-hexodiulosonate and by the enzymatic products of unsaturated digalacturonate but not by the digalacturonates. The KduD- strains lacked the dehydrogenase activity but in the presence of the digalacturonates produced higher levels of pectate lyase, polygalacturonase, and oligogalacturonate lyase than the KduD+ parents did. In the KduD- strains, pectate lyase and oligogalacturonate lyase were induced by unsaturated digalacturonate in a "gratuitous" manner, suggesting an intracellular accumulation of the inducer(s). We conclude that an intermediate(s) of the ketodeoxyuronate pathway induces pectate lyase, polygalacturonase, oligogalacturonate lyase, and ketodeoxyuronate dehydrogenase in E. chrysanthemi.
Yoga for cancer patients and survivors.

BACKGROUND Yoga has been practiced for thousands of years to improve physical and emotional well-being. Empirical research on yoga has been ongoing for several decades, including several recent studies conducted with cancer patients and survivors. METHODS This review provides a general introduction to yoga and a detailed review of yoga research in cancer. RESULTS Nine studies conducted with cancer patients and survivors yielded modest improvements in sleep quality, mood, stress, cancer-related distress, cancer-related symptoms, and overall quality of life. Studies conducted in other patient populations and healthy individuals have shown beneficial effects on psychological and somatic symptoms, as well as other aspects of physical function. CONCLUSIONS Results from the emerging literature on yoga and cancer provide preliminary support for the feasibility and efficacy of yoga interventions for cancer patients, although controlled trials are lacking. Further research is required to determine the reliability of these effects and to identify their underlying mechanisms.
The Expression of Ribonucleotide Reductase M2 in the Carcinogenesis of Uterine Cervix and Its Relationship with Clinicopathological Characteristics and Prognosis of Cancer Patients

Background To investigate the implication of ribonucleotide reductase M2 (RRM2) in the carcinogenesis of uterine cervix and its relationship with clinicopathological characteristics and prognosis of cancer patients. Methodology and Principal Findings The impact of RRM2 on cell viability was investigated in SiHa cervical cancer cells after RRM2 knockdown and the addition of cisplatin, which induces inter- and intra-strand DNA crosslinks. RRM2 immunoreactivity was evaluated by semi-quantitative H score among 29 normal, 30 low-grade dysplasia, 30 high-grade dysplasia and 103 invasive cancer tissue specimens of the uterine cervix, using tissue microarrays. RRM2 was then correlated with the clinicopathological variables of cervical cancer and patient survival. A greater toxic effect on cell viability using cisplatin was reflected by the greater reduction in RRM2 protein expression in SiHa cells. The RRM2 expression in cancer tissues was higher than that in high-grade dysplasia, low-grade dysplasia or normal cervical tissues. RRM2 upregulation was correlated with deep stromal invasion, large tumors and parametrial invasion and predicted poor survival. Conclusions RRM2 is a new molecular marker for the diagnosis and clinical outcomes of cervical cancer. It is involved in cervical carcinogenesis and predicts poor survival, and may be a potential therapeutic target including in cisplatin treatment.
Single amino acid substitutions in the N‐terminus of Vibrio cholerae TcpA affect colonization, autoagglutination, and serum resistance

The toxin‐coregulated pilus (TCP) of Vibrio cholerae O1 is required for successful infection of the host. TcpA, the structural subunit of TCP, belongs to the type IV family of pilins, which includes the PilE pilin of Neisseria gonorrhoeae. Recently, single amino acid changes in the N‐terminus of PilE were found to abolish autoagglutination in gonococci. As type IV pilins demonstrate some similarities in function and amino acid sequence, site‐directed mutagenesis and allelic exchange were used to create corresponding mutations in TcpA. All four mutant strains demonstrated autoagglutination defects, and all were highly defective for colonization in the infant mouse model. These results support the previously proposed correlation between autoagglutination and colonization. Finally, all four mutants are serum sensitive, indicating that TcpA plays a role in serum resistance, a phenotype previously attributed to TcpC. As the mutations have similar effects in N. gonorrhoeae and V. cholerae, our results support the idea that type IV pilins have similar functions in a variety of pathogenic bacteria.
Classifying musculocutaneous nerve variations

A total of 56 upper limbs from fetuses and adult cadavers were dissected to record anatomical variations in the musculocutaneous nerve (MC). A systematic literature review was performed to identify current classifications of MC variations. Communications were seen between the MC and median nerves in 53.6% of the dissections from which 84.6% were proximal, 7.7% distal, and 7.7% had one proximal and one distal communication to the point of entry of the MC into coracobrachialis muscle. In six out of 54 dissections where the MC was present, the nerve did not pierce the coracobrachialis muscle. In two cases, the MC was absent and in one case the MC and the median nerve had a distal origin. This article describes current classifications of MC variations and their problems. A new classification is proposed combining preexisting ones into an integrated and more detailed overview. Clinical manifestations of isolated MC injury with and without the presence of anatomical variations are thoroughly discussed. The knowledge of these variations will allow physicians to correctly interpret anomalous innervation patters of the upper limb. Clin. Anat. 22:671–683, 2009. © 2009 Wiley‐Liss, Inc.
Transcription of the Caveolin-1 Gene Is Differentially Regulated in Lung Type I Epithelial and Endothelial Cell Lines

In the lung, caveolin-1 is expressed in both type I alveolar epithelial and endothelial cells where it is hypothesized to modulate molecular signaling activities and progression of tumorigenesis. Developmentally, caveolin-1α is expressed in fetal lung endothelial, but not epithelial, cells; in adult lung, both cell types express caveolin-1α. To test the hypothesis that caveolin-1 transcription is differentially regulated in type I and endothelial cells, we characterized the proximal promoter of the mouse caveolin-1 gene in lung cell lines to identify factors that control its cell-specific expression. We show that caveolin-1 expression is regulated by an Ets cis-element in a lung epithelial cell line, but not a lung endothelial cell line, and that three ETS family members, ETS-1, PEA3, and ERM, recognize and bind the Ets site in the epithelial cell line. Based on these findings, we have identified the Ets cis-element as a region that accounts for differential transcriptional regulation of caveolin-1 in lung epithelial and endothelial cells.
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons

Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. We developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. The operon predictions are based on inter-genic distances. Our system can use different kinds of thresholds to accept a functional relationship, either related to the prediction of operons, or to the number of non-redundant genomes that support the associations. We also work by shells, meaning that we decide on the number of linking iterations to allow for the complementation of related gene sets. The method shows high reliability benchmarked against knowledge-bases of functional interactions. We also illustrate the use of Nebulon in finding new members of regulons, and of other functional groups of genes. Operon rearrangements produce thousands of high-quality new interactions per prokaryotic genome, and thousands of confirmations per genome to other predictions, making it another important tool for the inference of functional interactions from genomic context.
Review of methods to predict solder joint reliability under thermo-mechanical cycling

Solder joints are often the cause of failure in electronic devices, failing due to cyclic creep induced ductile fatigue. This paper will review the modelling methods available to predict the lifetime of SnPb and SnAgCu solder joints under thermo-mechanical cycling conditions such as power cycling, accelerated thermal cycling and isothermal testing, the methods do not apply to other damage mechanisms such as vibration or drop-testing. Analytical methods such as recommended by the IPC are covered, which are simple to use but limited in capability. Finite element modelling methods are reviewed, along with the necessary constitutive laws and fatigue laws for solder, these offer the most accurate predictions at the current time. Research on state-of-the-art damage mechanics methods is also presented, although these have not undergone enough experimental validation to be recommended at present.
Multi-User Cooperative Base Station Systems With Joint Precoding and Beamforming

Interference among multiple base stations that coexist in the same location limits the capacity of wireless networks. In this paper, we propose a method to design a single/multi-stream multi-user multiple-input multiple-output (MIMO) cooperative downlink transmission scheme employing precoding and beamforming under both the per base station (BS) and total BS power constraints. The per BS and total BS power constraints are the constraints where the power for each BS and all BSs is limited to a particular value, respectively. The algorithm eliminates the interference and achieves symbol-error rate (SER) fairness among different users. To eliminate the interference, Tomlinson-Harashima precoding (THP) is used to cancel part of the interference while the transmit-receive antenna weights cancel the remaining part. An iterative method based on the uplink-downlink duality principle is used to generate the transmit-receive antenna weights. The algorithm provides an equal signal-to-interference-plus-noise-ratio (SINR) across all users and reduces its computational complexity by trading off the complexity for a slight performance degradation. The proposed methods are extended to the scenario when the receiver does not have complete channel state informations (CSIs). Lastly, we propose a new method of selecting the user precoding order, which has a much lower complexity than VBLAST ordering but with almost the same performance. The simulation results show that the proposed schemes considerably outperform existing nonlinear and linear cooperative transmission schemes in terms of SER performance and approach an interference free performance.
CSSV: towards a realistic tool for statically detecting all buffer overflows in C

Erroneous string manipulations are a major source of software defects in C programs yielding vulnerabilities which are exploited by software viruses. We present C String Static Verifyer (CSSV), a tool that statically uncovers all string manipulation errors. Being a conservative tool, it reports all such errors at the expense of sometimes generating false alarms. Fortunately, only a small number of false alarms are reported, thereby proving that statically reducing software vulnerability is achievable. CSSV handles large programs by analyzing each procedure separately. To this end procedure contracts are allowed which are verified by the tool.We implemented a CSSV prototype and used it to verify the absence of errors in real code from EADS Airbus. When applied to another commonly used string intensive application, CSSV uncovered real bugs with very few false alarms.
Day Persons, Night Persons, and Time of Birth: Preliminary Findings

Abstract The authors conducted 2 surveys to determine the relationship between time of birth and being a day person or a night person. Day persons are most alert during daylight hours; night persons are most alert during hours of darkness. In Survey 1, the authors asked U.S. high school students to complete the Alertness Questionnaire (B. Wallace, 1993) and to respond to other items related to daytime or nighttime activity. In Survey 2, the authors administered the same items to a U.S. college population. In both surveys, time of birth was significantly related to being a day person or a night person. The results suggest that a critical period for setting the biological clock for alertness may be the moment of birth.
AR Puppet: Animated Agents in Augmented Reality

AR Puppet is a hierarchical animation framework for Augmented Reality agents, which is a novel research field connecting Augmented Reality (AR), Sentient Computing and Animated Agents to a single coherent human-computer interface paradigm. This framework enables the control of the physical environment and virtual animated agents using the same interface, blurring the boundary between the real and virtual world. Any physical object that can be monitored or controlled by a computer can be incorporated into the framework and used in AR applications. AR Puppet explores the requirements for context-aware animated agents concerning visualization, appearance, behavior, as well as associated technology and application areas. The framework is built on a powerful collaborative AR middleware and it allows for experimentation with a wide range of applications and many different characters – physical and virtual alike.
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In this paper, we explore a novel bilingual word alignment approach based on DNN (Deep Neural Network), which has been proven to be very effective in various machine learning tasks (Collobert et al., 2011). We describe in detail how we adapt and extend the CD-DNNHMM (Dahl et al., 2012) method introduced in speech recognition to the HMMbased word alignment model, in which bilingual word embedding is discriminatively learnt to capture lexical translation information, and surrounding words are leveraged to model context information in bilingual sentences. While being capable to model the rich bilingual correspondence, our method generates a very compact model with much fewer parameters. Experiments on a large scale EnglishChinese word alignment task show that the proposed method outperforms the HMM and IBM model 4 baselines by 2 points in F-score.
Asymmetric interactions in symmetric multi-core systems: Analysis, enhancements and evaluation

Multi-core architectures have spurred the rapid growth in high-end computing systems. While the vast majority of such multi-core processors contain symmetric hardware components, their interaction with systems software, in particular the communication stack, results in a remarkable amount of asymmetry in the effective capability of the different cores. In this paper, we analyze such interactions and propose a novel management library called SyMMer (Systems Mapping Manager) that monitors these interactions and dynamically manages the mapping of processes on processor cores to transparently improve application performance. Together with a detailed description of the SyMMer library, we also present performance evaluation comparing SyMMer to a vanilla communication library using various micro-benchmarks as well as popular applications and scientific libraries. Experimental results demonstrate more than a two-fold improvement in communication time and 10-15% improvement in overall application performance.
Intestinal Parasitic Infestation in Combatants and Their Families: A Hospital-Based Study in Mid-Western Regional Police Hospital, Nepal

Objective: To find out the scenario of intestinal parasitic infestation in combatants and their families in the setting of Mid-Western Regional Police Hospital (MWRPH), Nepal. Study Design: Cross-sectional study. Methods: All 2005 patients presented with the complaint of abdominal pain, diarrhoea, frequent defecation, blood in stool, or black stool from August 2007 to February 2011 were offered a stool examination. About 10g of fresh stool was collected in a clean, dry bottle. Two slides from each specimen were examined applying light microscope in 10 and 40 uvf at Banke, Nepalgunj hospital laboratory. Result: Among 2005 patients, 928 (46.28%) were infested with either helminths and/or protozoa. 96% were single infestation. The most common infestation was Ascaris lumbricoides (48.06%) and the second was hook worm (18.97%). Most common protozoal infestations were Entamoeba histolytica (12.92%) and Giardia lamblia (9.49%). Helminthic infestations peaked in cool months and protozoal infestations were rather steady throughout the year. Conclusion: Very high parasitic infestation in least developed mid- western Nepal may need urgent public health intervention.
Neonatal outcome in meconium stained amniotic fluid-one year experience.

OBJECTIVES To determine the effect of clear liquor and meconium stained liquor on mode of delivery, and to evaluate neonatal outcome. METHODS It was a Cross sectional analytical study, conducted in the department of Obstetrics and Gynaecology, Shaikh Zyed Federal Postgraduate Medical Institute/Hospital, Lahore and Shaikh Zaid Women Hospital Larkana, from April 2006 to March 2007. Two hundred and fifty patients from Larkana and 250 patients from Lahore in clear liquor group were included in the study. Similarly 125 patients from each city, that is 250 patients which had meconium stained liquor were included in group 2. The subjects with meconium stained amniotic fluid and clear amniotic fluid were registered as group 1 and 2. The socio demographic information, fertility history and gestational age of subjects were recorded. The investigations and information regarding mode of delivery and duration of labour were also noted. All babies delivered were attended by paediatricians. RESULTS In this study 500 cases with clear liquor and 250 cases of meconium stained liquor were selected from two cities, Lahore and Larkana. Out of these 55 (22%) patients had grade I meconium stained liquor, 140 (56%) patients and 55 (22%) patients had grade II and grade III meconium stained liquor respectively. The mode of delivery is significantly affected by meconium staining of liquor. The effect of meconium stained liquor was significant on time of delivery. There were 40 (16%) post date deliveries in meconium stained liquor as compared to 1% in subjects with clear liquor. The effect of meconium staining of liquor was significant on Apgar score, neonatal admission, meconium aspiration syndrome and neonatal deaths. CONCLUSION Meconium stained amniotic fluid (MSAF), is associated with increased neonatal morbidity and mortality. Caesarean sections were performed twice as frequently in women presenting with MSAF.
A Keyphrase-Based Approach to Summarization : the LAKE System at DUC-2005

The paper reports on LAKE participation at DUC-2005. We propose to exploit a keyphrase extraction methodology in order to identify relevant terms in the document. Afterward, a score mechanism is used to score the best sentences for each cluster of documents. At its heart, the LAKE algorithm first considers a number of linguistic features to extract a list of well motivated candidate keyphrases, then uses a machine learning framework to select significant keyphrases for a document. With respect to other approaches to keyphrase extraction, LAKE makes use of linguistic processors such as named entities recognition, which are not usually exploited. We discuss results and comment on both human assessment (Linguistic Quality and Responsiveness of the summaries), the ROUGE based evaluation, and the Pyramid evaluation.
Oral acetyl-L-carnitine therapy reduces fatigue in overt hepatic encephalopathy: a randomized, double-blind, placebo-controlled study.

BACKGROUND Fatigue is frequently reported in hepatic encephalopathy (HE) and may be related to hyperammonemia. Acetyl-L-carnitine (ALC) offers neuroprotective benefits and improves mitochondrial energetics and function. OBJECTIVE This study evaluated the effect of exogenous ALC on physical and mental fatigue, fatigue severity, and physical activity in patients with mild and moderate hepatoencephalopathy (HE1 and HE2, respectively). DESIGN A total of 121 patients with overt HE were recruited to the study and were subdivided into 2 groups according to their initial HE grade [HE1 (n = 61) or HE2 (n = 60)]. Thirty-one patients with HE1 and 30 with HE2 received 2 g ALC, and 30 patients with HE1 and 30 patients with HE2 received placebo twice a day for 90 d. All patients underwent clinical and laboratory assessments and automated electroencephalogram analysis. RESULTS At the end of the study period, the ALC-treated patients in the HE1 group showed significantly better improvement than did the placebo group in mental fatigue score (-1.7 compared with -0.3; P < 0.05), the fatigue severity scale (-6.4 compared with 2.3; P < 0.001), 7-d Physical Activity Recall questionnaire score (17.1 compared with -2.5; P < 0.001), and Short Physical Performance Battery (2.1 compared with 0.2; P < 0.001); the HE2 group showed significantly better improvement in the fatigue severity scale (-8.1 compared with -5.1; P < 0.001) and 6-min walk test (19.9 compared with 2.3; P < 0.05). Significant decreases in NH(4)(+) were observed in both groups (P < 0.001). CONCLUSION Patients with HE treated with ALC showed a decrease in the severity of both mental and physical fatigue and an increase in physical activity. This trial was registered at clinicaltrials.gov as NCT01223742.