Miracle-dz/UniFAR-FTUs huggingface dataset:
Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

Different protein secondary structure elements have different physicochemical properties and roles in the protein, which may determine their evolutionary flexibility. However, it is not clear to what extent protein structure affects the way Darwinian selection acts at the amino acid level. Using phylogeny-based likelihood tests for positive selection, we have examined the relationship between protein secondary structure and selection across six species of Drosophila. We find that amino acids that form disordered regions, such as random coils, are far more likely to be under positive selection than expected from their proportion in the proteins, and residues in helices and β-structures are subject to less positive selection than predicted. In addition, it appears that sites undergoing positive selection are more likely than expected to occur close to one another in the protein sequence. Finally, on a genome-wide scale, we have determined that positively selected sites are found more frequently toward the gene ends. Our results demonstrate that protein structures with a greater degree of organization and strong hydrophobicity, represented here as helices and β-structures, are less tolerant to molecular adaptation than disordered, hydrophilic regions, across a diverse set of proteins.
Botnet behaviour analysis: How would a data analytics‐based system with minimum a priori information perform?

Botnets, as one of the most aggressive threats, has used different techniques, topologies, and communication protocols in different stages of their lifecycle since 2003. Hence, identifying botnets has become very challenging specifically given that they can upgrade their methodology at any time. Various detection approaches have been proposed by the cyber‐security researchers, focusing on different aspects of these threats. In this work, 5 different botnet detection approaches are investigated. These systems are selected based on the technique used and type of data used where 2 are public rule–based systems (BotHunter and Snort) and the other 3 use machine learning algorithm with different feature extraction methods (packet payload based and traffic flow based). On the other hand, 4 of these systems are based on a priori knowledge while one is using minimum a priori information. The objective in this analysis is to evaluate the effectiveness of these approaches under different scenarios (eg, multi‐botnet and single‐botnet classifications) as well as exploring how a system with minimum a priori information would perform. The goal is to investigate if a system with minimum a priori information could result in a competitive performance compared to systems using a priori knowledge. The evaluation is shown on 24 publicly available botnet data sets. Results indicate that a machine learning–based system with minimum a priori information not only achieves a very high performance but also generalizes much better than the other systems evaluated on a wide range of botnet structures (from centralized to decentralized botnets).
Different modes of enhancer-specific regulation by Runt and Even-skipped during Drosophila segmentation

Expression of the Drosophila slp1 gene depends on nonadditive interactions between two cis-regulatory enhancers. These enhancers are repressed by preventing either Pol II recruitment or release of promoter-proximal paused Pol II in a manner that is both enhancer and transcription factor specific and can account for their nonadditive interaction.
S100A Protein Expression in the Distinction Between Lentigo Maligna and Pigmented Actinic Keratosis

Lentigo maligna (LM), a type of malignant melanoma in situ, and pigmented actinic keratosis (PAK) may have similar clinical appearances but are different in prognosis and treatment. Diagnosis is established by skin biopsy. In certain cases, microscopic features may be very similar in both entities, making it difficult to determine whether the pigmented atypical cells are keratinocytes or melanocytes. Immunohistochemical markers can be useful for the identification of melanocytes in these cases. There are limitations to the use of some standard immunohistochemistry markers, however. S100 proteins are a varied group of proteins that are of special interest because of their dysregulated expression in neoplastic disorders. Their expression is changed during malignant transformation, progression, and/or metastasis in various cell lines and tumors, including melanomas. Our study analyzed the expression of several of the S100 protein subtypes (S100A2, S100A6, and S100A8/A9 or A12) in 38 LM cases and 44 PAK cases to define their potential value in the distinction between these entities together with their role in the development of early malignant melanoma of the skin. The results showed an upregulation of S100A2 protein in atypical keratinocytes in PAK and in normal keratinocytes adjacent to melanoma cells in LM. There was also an upregulation of S100A8/A9 or A12 protein, as detected by the antibody MAC387, in normal keratinocytes adjacent to both atypical keratinocytes and melanocytes in PAK and LM, respectively. There were statistically significant differences in the level of positive cells and in the pattern of immunoreactivity for anti-S100A2 and MAC387 in each entity, however. Moreover, the findings of our study support the notion that melanocyte-keratinocyte interactions are abnormal in both of these disease entities and may be involved in their progression.
Depleted Uranium Radioactive Contamination In Iraq : An Overview

Depleted Uranium (DU) weaponry has been used against Iraq for the first time in the history of recent wars. The magnitude of the complications and damage related to the use of such radioactive and toxic weapons on the environment and the human population mostly results from the intended concealment, denial and misleading information released by the Pentagon about the quantities, characteristics and the area’s in Iraq, in which these weapons have been used. Revelation of information regarding what is called the Gulf War Syndrome among exposed American veterans helped Iraqi researchers and Medical Doctors to understand the nature of the effect of these weapons, and the means required to investigate further into this issue. The synergetic impact on health due to the post Gulf War I economical sanctions and DU related radioactive contamination raised the number of casualties in contaminated areas as in southern Iraq. Continual usage of DU after Gulf War I on other Iraqi territories through the illegal No-Fly Zones and the major DU loaded Cruise Missiles attack of year 1998, all contributed in making the problem increasingly complex. During 2003, military operations conducted in Iraq by the invading forces used additional rounds of DU in heavily populated areas such as Baghdad, Samawa and other provinces. It is only fair to conclude that the environment in Iraq and its population have been exposed continuously to DU weaponry or its contaminating remains, since 1991. Accordingly millions of Iraqi’s have received higher doses of radioactivity than ordinary background levels. As a result a multi-fold increase of low level radiation exposure related diseases have been registered since 1995. An increase of children’s leukemia, congenital malformations, breast cancer etc. The shift of leukemia incidence rates towards younger children during the recent years, and its association with geographically distributed contaminated areas, offers strong evidence of the correlation between LLR exposure and resulted health damages. Through this paper, an overview of major scientific DU conclusions will be presented, drawn from investigations and research conducted since the year 1991 by Iraqi researchers and MDs. Schemes of these researches can be classified into three categories: 1. DU contamination detection and exploration programs. 2. DU effects on human body cells. 3. DU related epidemiological studies.
SAT-Based Abductive Diagnosis

Increasing complexity and magnitude of technical systems demand an accurate fault localization in order to reduce maintenance costs and system down times. Resting on solid theoretical foundations, model-based diagnosis provides techniques for root cause identification by reasoning on a description of the system to be diagnosed. Practical implementations in industries, however, are sparse due to the initial modeling effort and the computational complexity. In this paper, we utilize a mapping function automating the modeling process by converting fault information available in practice into propositional Horn logic sentences to be used in abductive model-based diagnosis. Furthermore, the continuing performance improvements of SAT solvers motivated us to investigate a SAT-based approach to abductive diagnosis. While an empirical evaluation did not indicate a computational benefit over an ATMS-based algorithm, the potential to diagnose more expressive models than Horn theories encourages future research in this area.
Comminution of logging residues with a tub grinder: Calculation of productivity and procurement cost of wood chips

Nacrtak An experiment on comminution of logging residues with a tub grinder was carried out in order to calculate the productivity and procurement cost of wood chips. At the investigated site, the tub grinder had a hammer mill crusher at the bottom of the tub, and a grapple loader and a bucket loader worked as auxiliary machines for the grinder. As a result, the productivity of the tub grinder was 60.0 loose m/PMH0, and the total comminuting cost was calculated as 5.637 US$/m3, indicating that the comminuting cost of a large-sized crusher was lower than that of a small-sized chipper. The percentage of the cost of loaders, that of carrying in, installing, and carrying out the machines, and that of constructing a landing was 53% of the total comminuting cost. When a truck with the capacity of 40 m3 transported wood chips three times a day, the costs of comminution and transportation were 71.2 US$/t (DM1), which is almost on a par with those of European countries in which the energy utilization of logging residues is making steady progress. As a result of the discussion about the balance between the processing capacity of the tub grinder and that of other machines, it seemed reasonable for Japanese forestry to consider the use of one tub grinder at several logging sites.
‘I call it the blame and shame disease’: a qualitative study about perceptions of social stigma surrounding type 2 diabetes

Objectives While health-related stigma has been the subject of considerable research in other conditions (obesity and HIV/AIDS), it has not received substantial attention in diabetes. The aim of the current study was to explore the social experiences of Australian adults living with type 2 diabetes mellitus (T2DM), with a particular focus on the perception and experience of diabetes-related stigma. Design A qualitative study using semistructured interviews, which were audio recorded, transcribed and subject to thematic analysis. Setting This study was conducted in non-clinical settings in metropolitan and regional areas in the Australian state of Victoria. Participants were recruited primarily through the state consumer organisation representing people with diabetes. Participants All adults aged ≥18 years with T2DM living in Victoria were eligible to take part. Twenty-five adults with T2DM participated (12 women; median age 61 years; median diabetes duration 5 years). Results A total of 21 (84%) participants indicated that they believed T2DM was stigmatised, or reported evidence of stigmatisation. Specific themes about the experience of stigma were feeling blamed by others for causing their own condition, being subject to negative stereotyping, being discriminated against or having restricted opportunities in life. Other themes focused on sources of stigma, which included the media, healthcare professionals, friends, family and colleagues. Themes relating to the consequences of this stigma were also evident, including participants’ unwillingness to disclose their condition to others and psychological distress. Participants believed that people with type 1 diabetes do not experience similar stigmatisation. Conclusions Our study found evidence of people with T2DM experiencing and perceiving diabetes-related social stigma. Further research is needed to explore ways to measure and minimise diabetes-related stigma at the individual and societal levels, and also to explore perceptions and experiences of stigma in people with type 1 diabetes.
Hmong Students in Higher Education and Academic Support Programs

Student awareness, usage, and perception of academic support programs were examined among 55 Hmong college students at a large, public western university. Twenty-eight students had participated in one or more ASPs while 27 students had not participated in any ASPs. Those who had participated found the programs to be supportive with an average rating of 7.39 out of 10 (10 being most supportive). The majority of students who did not participate in ASPs reported that they were not aware of ASPs and their services. Results also show that the majority of Hmong college students perceived a lack of time to study, poor study habits, lack of money, lack of motivation, lack of direction on career goals, and poor time management to be obstacles for them in higher education. Based on the findings, it seems ASPs were not able to reach some Hmong students with their outreach efforts. However, those that they were able to reach found academic support services helpful, especially with financial concerns and direction on career goals.
Nursing diagnoses (NANDA-I) in hematology-oncology: a Delphi-study.

PURPOSE To identify NANDA-I diagnoses that are most relevant to hematology-oncology nursing in Europe. METHODS In a two-round, electronic, quantitative Delphi study, 28 experts from nine European countries assessed the relevance of NANDA-I diagnoses and health problems. FINDINGS This study identified 64 relevant diagnoses and three health problems. All experts listed 11 diagnoses: "imbalanced nutrition: less than body requirements,""diarrhea,""fatigue,""risk for bleeding,""risk for infection,""impaired oral mucous membrane,""risk for impaired skin integrity,""impaired skin integrity,""hyperthermia,""nausea,""acute pain," and the health problem "pruritis. " CONCLUSIONS AND IMPLICATIONS FOR PRACTICE The "NANDA-I classification 2009-2011" describes, in almost all disease- and treatment-related problems, nursing diagnoses as relevant to the adult patient with hematological malignancy. These diagnoses are therefore recommended.
Writing in the company of other women: exceeding the boundaries

In academic life, writing for publication is a significant responsibility. It can also be a rewarding private pleasure. This article reports on the effects of attending week‐long writing retreats for a group of academic women in Aotearoa New Zealand. The residential retreats have been held twice a year since 1997, and attract women from different institutions, disciplines and at different stages in their careers. Through examining data gathered by open‐ended questionnaires, the author explores the effects of attending the retreats on the participants’ academic writing productivity and pleasure, and on their sense of themselves as academics and writers.
Sex differences in stress, illness and coping resources among the Nigerian elderly

Since studies have found only a moderate relationship between life change and illness, researchers have begun to study “coping resources” that facilitate adjustment to life events. Using a sample of 115 elderly residing in the small city of Awe in the Southwestern part of Nigeria, this study examines the relationship between life change and illness for each sex to determine if elderly men and women differ in their vulnerability to life change stress and to identify differences in what serves as a coping resource. The results suggest that elderly women are more responsive to life changes. For women, marriage and self-efficacy were exacerbators; for men, having a confidant exacerbated illness. Resources functioning as coping facilitators for young age groups potentially function as coping inhibitors when related to the largely negative/uncontrollable events of old age. In addition, the sexes may differ in the factors that serve as coping resources.
Shift Work, Safety, and Aging

It has long been recognized that older shift workers may have shorter and more disturbed day sleeps between successive night shifts than their younger colleagues. This has given rise to considerable concern over the safety of aging shift workers because of the increasing age of the work force and increases in retirement age. Because there have been no direct studies of the combined effects of shift work and age on safety, the present paper begins by reviewing the literature relating safety to features of shift systems. It then considers the general effect of age on occupational injury rates before examining existing evidence of the combined effects of shift work and age on performance capabilities. The results of the literature review indicate that when the a priori risk is constant, there is reasonably clear evidence that injury rates are higher at night, and that they increase over successive night shifts more rapidly than over successive day shifts. Further, although occupational injuries are less frequent in older workers, those that do occur tend to be more serious. Finally, there is some suggestive evidence from studies of objectively measured performance capabilities that older workers may be less able to both maintain their performance over the course of a night shift and cope with longer spans of successive night shifts. It is concluded that it seems possible, even though unproven as yet, that older workers may be at greater risk both to injury and accident on the night shift. There is a strong need for future epidemiological studies of the combined effects of shift work and age on injuries and accidents, and that these should attempt to separate the effects of age per se from those of generation.
Phase II study of docetaxel, doxorubicin, and cyclophosphamide as first-line chemotherapy for metastatic breast cancer.

PURPOSE This pilot phase II study investigated the efficacy and toxicity of docetaxel with doxorubicin and cyclophosphamide (TAC) as first-line chemotherapy for anthracycline-naive patients with metastatic breast cancer. PATIENTS AND METHODS Fifty-four patients received a total of 359 courses consisting of docetaxel 75 mg/m2 given intravenously (IV) over 1 hour, preceded by IV doxorubicin 50 mg/m2 and cyclophosphamide 500 mg/m2 for a maximum of eight 3-week cycles. RESULTS After an independent panel review, the overall objective response rate was 77% (complete response, 6%). Overall objective response rates in patients with visceral, bone, and liver involvement were 82%, 82%, and 80%, respectively. Median duration of response was 52 weeks, and median time to progression was 42 weeks. With a median follow-up of 32 months, the median survival had not yet been reached, whereas the 2-year survival was 57%. The main toxicities were hematologic (neutropenia grade 3/4 in 100% of patients and 95% of cycles; febrile neutropenia in 34% of patients and 9% of cycles). Documented grade 3 infection was seen in one patient (2%) in one cycle, and no toxic death was reported. Severe acute or chronic nonhematologic adverse events were infrequent, and docetaxel-specific toxicities (such as fluid retention and nail changes) were mild, with only one patient being discontinued for fluid retention. Congestive heart failure was seen in two patients (4%). CONCLUSION TAC is an active and manageable regimen that has been chosen as the basis of five randomized phase III trials, including two pivotal studies comparing TAC to fluorouracil plus doxorubicin and cyclophosphamide in the metastatic and adjuvant treatment of breast cancer.
The Type VI Secretion System Encoded in SPI-6 Plays a Role in Gastrointestinal Colonization and Systemic Spread of Salmonella enterica serovar Typhimurium in the Chicken

The role of the Salmonella Pathogenicity Islands (SPIs) in pathogenesis of Salmonella enterica Typhimurium infection in the chicken is poorly studied, while many studies have been completed in murine models. The Type VI Secretion System (T6SS) is a recently described protein secretion system in Gram-negative bacteria. The genus Salmonella contains five phylogenetically distinct T6SS encoded in differentially distributed genomic islands. S. Typhimurium harbors a T6SS encoded in SPI-6 (T6SSSPI-6), which contributes to the ability of Salmonella to colonize mice. On the other hand, serotype Gallinarum harbors a T6SS encoded in SPI-19 (T6SSSPI-19) that is required for colonization of chicks. In this work, we investigated the role of T6SSSPI-6 in infection of chicks by S. Typhimurium. Oral infection of White Leghorn chicks showed that a ΔT6SSSPI-6 mutant had reduced colonization of the gut and internal organs, compared with the wild-type strain. Transfer of the intact T6SSSPI-6 gene cluster into the T6SS mutant restored bacterial colonization. In addition, our results showed that transfer of T6SSSPI-19 from S. Gallinarum to the ΔT6SSSPI-6 mutant of S. Typhimurium not only complemented the colonization defect but also resulted in a transient increase in the colonization of the cecum and ileum of chicks at days 1 and 3 post-infection. Our data indicates that T6SSSPI-6 contributes to chicken colonization and suggests that both T6SSSPI-6 and T6SSSPI-19 perform similar functions in vivo despite belonging to different phylogenetic families.