bluuebunny/crossref_metadata_2025_split huggingface dataset:
DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components
Authors: Obermayer Alyssa , Chang Darwin , Nobles Gabrielle , Teng Mingxiang , Tan Aik-Choon , Wang Xuefeng , Eschrich Steven , Rodriguez Paulo , Grass G Daniel , Meshinchi Soheil , Tarhini Ahmad , Chen Dung-tsa , Shaw Timothy 
Published: March 2023

Abstract

Pathway-level survival analysis offers the opportunity to examine molecular pathways and immune signatures that influence patient outcomes. However, available survival analysis algorithms are limited in pathway-level function and lack a streamlined analytical process. Here we present a comprehensive pathway-level survival analysis suite, DRPPM-PATH-SURVEIOR, which includes a Shiny user interface with extensive features for systematic exploration of pathways and covariates in a Cox proportional-hazard model. Moreover, our framework offers an integrative strategy for performing Hazard Ratio ranked Gene Set Enrichment Analysis (GSEA) and pathway clustering. As an example, we applied our tool in a combined cohort of melanoma patients treated with checkpoint inhibition (ICI) and identified several immune populations and biomarkers predictive of ICI efficacy. We also analyzed gene expression data of pediatric acute myeloid leukemia (AML) and performed an inverse association of drug targets with the patient’s clinical endpoint. Our analysis derived several drug targets in high-risk KMT2A-fusion-positive patients, which were then validated in AML cell lines in the Genomics of Drug Sensitivity database. Altogether, the tool offers a comprehensive suite for pathway-level survival analysis and a user interface for exploring drug targets, molecular features, and immune populations at different resolutions.
Practice development in the late 80's and the veterinarian's role
Authors: Neubauer Gary D. 
Published: March 2023

Profitable livestock production and the veterinarian’s role. Will this be a challenge or an opportunity? Ask yourself—am I a necessary evil or a partner in profits? Practice development in the future will rely heavily on the expanded role of the veterinarian as a health specialist and not just as a disease specialist. The veterinarian’s image needs to be reviewed as a part of profits not losses of the livestock enterprise. Finally, the veterinarian’s role as a herd health specialist needs to be looked on as: 1) a leader who is knowledgeable and respected, 2) as a partner who is trusted and reliable, and 3) as a business manager who is profit oriented.
A successful health specialist will be one who can utilize this knowledge of medicine and production and effectively communicate these ideas in such a way that the client understands them, accepts them, and implements them to the fullest extent toward efficient, profitable production.
Reproductive endocrinology of the cow: Part 2
Authors: Yadav M. C. , Walton J. S. , Leslie K. E. 
Published: March 2023

In Part 1 the intricate hormonal relationships involved in the bovine estrous cycle were described. The widespread growth of the embryo transfer industry has made manipulation of reproductive events of both donors and recipients a commonplace practice in reproductive programs. This article presents a review of the various methods used to produce a superovulatory response in cows and the basic endocrinological changes which allow this response to occur.
Superovulation can be defined as the increased ovulatory response induced in an individual above the normal range of ovulation rates for that individual. In cattle, therefore, three or more ovulations are considered as superovulatory responses.
Bacteriological findings in nasal and lower respiratory tract samples of calves with acute respiratory disease
Authors: Viring S. , Boleske G. , Franklin A. , Rehbinder V. , Segal T. , Troedsson M. 
Published: March 2023

Infectious calf pneumonia passes off with high morbidity and is frequent in housed dairy animals in the winter. In Sweden the greatest disease problems occur in the “specialized calfrearing units” for meat production. To these farms about 100,000 calves (> 2 weeks old) are now mediated every year from dairy farms. Viral mycoplasmal and bacterial agents are involved in the complex etiology. From emergency slaughtered animals in Sweden Pasteurella multocida, Pasteurella multocida, Pasteurella hemolytica and Actinomyces pyogenes were the most commonly isolated bacteria. Mycoplasma dispar was the most commonly mycoplasmal species isolated. No investigation has been performed in Sweden over bacteria present in the lower respiratory tract at the acute phase of calf pneumonia.
The aim of the present study was to compare the bacteriological flora in the nasal cavity with that of the lower respiratory tract in diseased animals and in healthy animals.
Johne's disease in cattle
Authors: Sweeney Raymond W. , Whitlock Robert H. 
Published: March 2023

Paratuberculosis (Johne's disease) occurs worldwide and is widespread in the United States. A slaughter survey in cows from northeastern states estimated the prevalence of paratuberculosis in cull dairy cows at 7.3% and a similar survey in Wisconsin revealed a 10.8% prevalence.
Economic losses due to paratuberculosis may include decreased milk production, premature culling, and increased susceptibility to other diseases. In Pennsylvania alone, over 500 herds positive for Johne's disease have been identified with economic losses estimated at $5.8 million annually. Of the 10.8 million dairy cows in the U.S., nearly 1 million are thought to be affected, and the total losses due to paratuberculosis are expected to exceed $1.5 billion annually for the dairy industry in the United States.
Therapy for Johne's disease
Authors: Hoffsis Glen F. , Streeter Robert N. , Rings D. Michael , St. Jean Guy 
Published: March 2023

Several previous reports have described successful treatment of Johne's Disease but few, if any, have described successful embryo transfer during treatment. These cases illustrate that viable embryos could be transferred from cows while receiving isoniazid for the treatment of clinical Johne's Disease. Embryos were collected multiple times and resulted in normal calves being delivered. It is not known if any of the calves are infected but the probability of infection is low and all remained healthy.
Treatment of these cows did not eliminate infection or lesions as evidenced by consistently positive fecal cultures and biopsies during treatment and the periodic relapses.
Whether treatment was cost effective or not depends on the value of the progeny resulting from embryo transfers. Both owners have indicated they feel the effort was worthwhile.
Improving performance of cattle consuming medium or low quality forages
Authors: Wagner Donald G. 
Published: March 2023

Supplements often improve performance and/or profitability of grazing cattle. The goal should be to improve profit, not just performance. When forage quailty is high, supplementation needs are minimal; simply providing a source of minerals, vitamins, antibiotics and/or ionophores may often be adequate. The optimal items will depend upon the situation. This paper will not address the above items, but will address selected topics on protein supplementation.
What about feeding protein or perhaps energy supplements to cattle on pasture or when feeding harvested roughages? Protein and/or energy supplementation may be justified or may improve performance and profitability in a variety of cases. Usually, protein supplementation is more likely to be profitable or cost effective under a wider variety of grazing conditions than is energy supplementation (i.e. merely feeding supplemental grain). Therefore, this article will be devoted primarily to a discussion of some aspects of protein supplementation which offer excellent potential for increasing profits.
Coenuriasis in cattle
Authors: Thomas Islwyn 
Published: March 2023

Although coenuriasis in cattle is referred to in textbooks, it is less common than in sheep, and is possibly not considered in the differential diagnosis of nervous disorders of cattle in most areas of the United Kingdom. (Greig and Holmes, 1977).
Coenuriasis (local names: Gid, Bendro, Sturdy, Tuatheal) is the disease caused by invasion of the brain and occasionally the spinal cord by the cystic larval stage of Taenia multiceps, a tapeworm of the dog and fox (Williams, 1976; Edwards et al., 1979). The localized space-occupying lesion of the CNS usually results in death of the host unless treated surgically.
Anaesthesia in cattle (II)
Authors: Jones R. S. 
Published: March 2023

Whilst a number of techniques of regional or local analgesia have been described in cattle many years ago, there are a number of others which have only been described recently or have been "rediscovered" and/or modified. The well tried techniques include cornual nerve block, paravertebral nerve block, epidural analgesia and the Raker technique for analgesia of the distal limbs.
It is considered essential to ensure that cattle are adequately sedated and restrained for the application of local analgesic techniques and for the period when surgery is being carried out. This is to prevent damage or injury to the surgeon, assistant and/or animal and to ensure that whilst perhaps not totally aseptic, the surgery is carried out in as clean a manner as possible. The actual techniques of sedation have been described in the earlier paper.
Reduction of dislocated hips
Authors: Reynolds I. B. 
Published: March 2023

Most veterinarians in dairy practice will have been presented with a cow with a coxofemoral luxation (commonly known as dislocated hip) usually either over the calving period, related to calving paralysis, milk fever etc., or more commonly, during the mating period when cows riding each other on the cow yard slip, spread their legs abnormally and dislocate their hip joints.
During my time in dairy practice, I have developed methods of diagnosis, prognosis and reduction of the dislocated hip. I have had as many reduction failures as I have had successes, but all cases help my understanding and knowledge of hip dislocation and the successes make me keep trying.
Understanding cow behavior
Authors: Roberts John 
Published: March 2023

Understanding cow behavior, and behavioral responses to stress of any origin, is important when attempting to interpret the effects of stray voltage on a dairy farm. Some behaviors can become detrimental to health and production even if the cause of the behavior change does not directly result in damage. The essential message to understand is that the behaviors commonly considered as indications of stray voltage are general behavior responses. These changes should not be considered specific to stray voltage. This is particularly relevant in cases where stray voltage is resolved, but abnormal behaviors do not decrease.
Abnormal or undesired animal behaviors usually have their origins in the very basic psychological makeup of an animal. The performance of the animal behaviors commonly associated with the occurrence of stray voltageare generalized behavioral expressions that are likely to come from a variety of electrical and non-electrical stresses. Behaviors such as lapping at the water cup, weight shifting, tail switching, nose pressing, kicking,self destructive heifer syndrome, and a general unthriftiness or apathy in the herd may be perceived asbeing caused by stray voltage. Certainly some of these behaviors are increased by stray voltage, but their origin can also be from non-electrical stresses.
Conception rate of lactating dairy cows using ovsynch after presynchronization with prostaglandin F2α (PGF2α) or Gonadotropin Releasing Hormone (GnRH)
Authors: Bartolome J.A. , Sheerin P. , Luznar S. , Melendez P. , Kelbert D. , Risco C.A. , Thatcher W.W. , Archbald L.F. 
Published: March 2023

This study compared the pregnancy rate in cows inseminated after two different pre-synchronization protocols based on clinical features of the genital tract and treatment with either PGF2α or GnRH. A total of 340 reproductively normal lactating dairy cows was divided in two groups. Cows in Group 1 (n=216) had a corpus luteum when palpated per rectum on day 0. These cows were administered 25 mg of PGF2α on day 0, 100υg ofGnRH on day 14, 25 mg of PGF2α on day 21, 100 υg of GnRH on day 23, and time-inseminated 16-h later. Cows detected in estrus from day Oto day 14 were inseminated 10 to 12-h after signs of estrus.
Cows in Group 2 (n=124) either had a large ovarian follicle and uterine tone, or a corpus hemorragicum whenpalpated per rectum on day 0. These cows received 100 υg of GnRH on day 0, 100 υg of GnRH on day 8, 25 mg of PGF2α on day 15, 100 υg of GnRH on day 17, and time-inseminated 16-h later. Cows detected in estrus before the end of the treatment protocol were inseminated 10 to 12-h after signs of estrus and removed from the study. Data collected were pregnancy rate for cows time-inseminated in Group 1, cows inseminated at detected estrus in Group 1, and cows time-inseminated in Group 2. Pregnancy rates were compared using logistic regression adjusted for number of previous services, parity, season and days in milk. There was no difference (p=0.83) in pregnancy rate between cows time-inseminated in Group 1 (35.9%) and Group 2 (32.8%). In Group 1, there was no difference (p=0.21) in pregnancy rate between cows time-inseminated (35.9%) and cows inseminated at detected estrus within 14-d after treatment with PGF2α (43.5%). Results of this study suggest that cows in different stages of the estrous cycle, as determined by rectal palpation of the genital tract, had similar pregnancy rates when they were selectively pre-synchronized with either PGF2α or GnRH.
Explaining earnings variation of bovine veterinarians in private practice
Authors: Dodge Lynn E. , Koontz Stephen R. 
Published: March 2023

Bovine veterinarians are needed to protect food animal protein supplies, prevent losses due to disease, and protect public health: society needs these services. It is also important that economic incentives exist for, and are understood by, practitioners that serve the food animal industry. Surveys of American Association of Bovine Practitioners members were examined to explain variation in bovine veterinary earnings in private practice. We estimate the systematic variation in earnings due to practitioner characteristics. Results communicate expected earnings levels and variation across bovine veterinarians in private practice based on observable individual attributes and characteristics. These results communicate, in context of the survey questions, what the market for bovine veterinary services values. Bovine veterinarians are compensated more for specializing in a species within the food animal industries and owning their practice. The volume of animals seen is important, and bovine veterinarians should look to practice in areas with large concentrations of animals. Numbers of clients attained are not important, whereas numbers of animals serviced are. Further, gaining experience is more important than additional education or certifications beyond the doctor of veterinary medicine degree. However, there remains a large unexplainable variation in earnings models. This unexplained variation is likely due to unobserved and unmeasured ability/effort effects within each individual and it is thought, but not tested, that higher quality veterinarians earn more. Future salary surveys need to attempt to measure these deep human capital attributes.
Single-breath diffusion capacity of the lungs for carbon monoxide in children with cystic fibrosis: methods of interpreting results
Authors: Bystrova S. G. , Simonova O. I. , Akhmedova E. E. , Kustova O. V. 
Published: March 2023

Introduction. Progression of pulmonary and heart failure often causes death in patients with cystic fibrosis (95%). Therefore, monitoring of lung condition is very important for patients with cystic fibrosis (CF). Structural changes are visualized by computed tomography of the chest (CT) and are scored using the Brody scale. For children older than 5 years, pulmonary function tests (PFTs) tests (which are evaluated in percent of predicted (%) values) are available, such as spirometry, body plethysmography (BP), diffusion capacity of the lungs (DL) test. The results of the single-breath (SB) DL for carbon monoxide test are DLCO-SB, alveolar volume (VA-SB) and their ratio (KCO-SB). In the presence of non-communicative zones for gas perfusion, VA-SB may not present true VA. For patients with CF, it is proposed to use VA determined by BP for calculating KCO-BP, or to adjust the predicted DLCO-SB and KCO-SB for VA.Aim. To assess the informativeness DLCO-SB, KCO-SB and KCO-BP in children with CF.Materials and methods. 28 children with CF (8–18 years old) were examined in the department of pulmonology of the National Research Center for Children’s Health. PFTs included DLCO-SB, spirometry and BP. Additionally, we evaluated the data of the blood gas and acid-base values, age, body mass index and CT scores.Results and discussion. We found that in most patients DLCO-SB and KCO-SB were within the normal range, and decreased in children older than 14 years with background of severe bronchiectasis.Conclusion. Thus, in children with CF the DL test is informative, and adjustment for VA is useful.
Quality of life in children after a new coronavirus infection
Authors: Isaeva E. P. , Zaytseva O. V. , Lokshina E. E. , Murtazaeva O. A. , Zaytseva S. V. , Sirota N. A. , Ponkratov D. A. , Zyabkin I. V. 
Published: March 2023

Introduction. After an infection with the SARS-CoV-2 virus, in some cases, the so-called post-covid syndrome is formed, which includes conditions and symptoms that develop during and / or after the disease, lasting more than 12 weeks, occurring in waves or on a permanent basis, and without a confirmed alternative diagnosis. Vegetative, psycho-emotional disorders, as well as disorders of the cardiovascular system, digestive and some others can be considered as manifestations of the post-covid syndrome. The variety of clinical manifestations of post-COVID syndrome in children can have a significant impact on their quality of life (QoL).Aim. To estimate the quality of life of children aged 5 to 17 years after COVID-19.Materials and methods. The study included 92 children aged 5 to 17 years, divided into two groups. The study group included 62 children (31 boys, 31 girls; mean age 12.0 (7.4; 14.5) years) after a new coronavirus infection. The control group consisted of 30 children who had acute respiratory tract infection of a different etiology and did not have COVID-19 (16 girls and 14 boys; mean age 12.5 (7.5; 15.1) years). The assessment of QoL in children of the study groups was carried out using the Russian version of the PedsQL 4.0 questionnaire. Parental and child forms of the questionnaire were used.Results. The average follow-up period after a coronavirus infection was 6 months (from 3 to 12 months). 92 patient questionnaires were analyzed: 14 in the group of children 5–7 years old, 36 in the group of children 8–12 years old, 42 in the group of children and adolescents 13–17 years old, and 14 parental questionnaires in the group of children 5–7 years old. The indicators of the quality of life of children after COVID-19 were statistically significantly reduced compared to the control group in all age groups. Differences in the assessment of the quality of life by preschool children and their parents were revealed.Conclusions. A significant decrease in the life quality was revealed in children with COVID-19 history after six months (3–12 months) of the disease manifestation in comparison with control group.
Prediction of bone metabolism disorders in premature babies
Authors: Druzhinina N. A. , Merzlyakova D. R. , Vakhitova G. A. , Gilyazova G. G. , Shakirova L. G. , Khayretdinova T. B. 
Published: March 2023

Introduction. Premature newborns suffer from osteopenia, which scientists attribute to vitamin D deficiency. Its deficiency leads to impaired development, the success of which depends on the first years of life. Given the increase in the number of premature babies born after in vitro fertilization, the question arises regarding the risk of them developing vitamin D deficiency.Aim to establish risk factors and develop prognostic tables for vitamin D deficiency in premature infants of the first three years of life born by in vitro fertilization and naturally.Materials and methods. We studied premature newborns (n = 189), which we divided into two groups, born by in vitro fertilization and naturally (comparison group). In each group, two subgroups of infants were identified. In the main in vitro fertilization group, the 1st subgroup included newborns weighing 1,000–1,500 g (n = 52), and the 2nd – weighing less than 1,000 g (n = 49). The comparison group included infants born naturally with a body weight of 1,000–1,500 g (n = 46) and those with a body weight of less than 1,000 g (n = 42).Results. Vitamin D deficiency was established in 67.7 ± 4.8% premature babies during the first year of life. In the second year of life, with intake of vitamin D 1000 IU/day, the level of calcidiol stabilized to normal value. The most sensitive group concerning vitamin D insufficiency is the group of babies with breast-milk substitutes. Factors associated with in vitro fertilization had not shown statistically significant influence on the vitamin D insufficiency in premature babies.Conclusion. We have proposed beneficial predictive tables for an individual risk evaluation of possible bone metabolic conditions in premature babies.
Nutritional support for different conditions accompanied with protein and energy insufficiency in children
Authors: Zakirova A. M. , Faizullina R. A. , Kadriev A. G. , Shayapova D. Т. , Palmova L. Yu. , Rashitova E. L. , Zaripov I. R. , Kadriev A. A. , Kiselеv R. P. 
Published: March 2023

Introduction. Malnutrition in children manifests itself in the form of general metabolic disorders and leads to impaired cellular differentiation of tissues. The state of nutritional status is an important success factor in the treatment of any disease, therefore, the development of methodological approaches to optimize the nutritional status of children with protein-energy malnutrition is an urgent task.Aim. To study the efficacy and safety of nutritional support in various conditions accompanied by protein-energy malnutrition in children.Materials and methods. 62 cases were analyzed: including 29 with antibiotic-associated diarrhea, 8 with celiac disease, 14 with gastrointestinal allergy (allergic enteropathy), 11 with hypostature against the background of low gestational age with birth. Age – 1–10 years. All patients were divided into groups identical in age, nosology, gender, duration of the pathological condition, degree of malnutrition. In the main group (31 children), the main treatment included a low-microbial diet, sips, parenteral nutrition with glucose-salt solutions (7–10 days), enteral nutrition. The control group consisted of 31 children, in whose therapy there was no enteral nutrition. Anthropometry, clinical, laboratory and instrumental examination were used to assess the nutritional status.Results and discussion. The main syndromes during treatment are: underweight, loss of appetite, intestinal dyspepsia and malabsorption. Analysis of the diet indicated the monotony of the set of products. The course of nutritional support was 15 days. The survey was conducted on the 1st, 5th, 10th, 15th days of the study. The effect of using enteral nutrition in terms of physical development, clinical and laboratory parameters was more significant in the main group compared to conventional methods of nutrition optimization.Conclusions. The use of enteral nutrition in combination with drug therapy shows more significant effectiveness compared to conventional methods of nutrition optimization.