nils-herrmann/clean_scirepeval huggingface dataset:
Comment on: A validated mathematical model of cell-mediated immune response to tumor growth.

Gowal et al. erroneously surmise that in ref. 1, we assume ‘‘unrealistic’’ initial natural killer (NK) cell levels of zero in order to generate the simulations of Fig. 4, and they conclude from their own simulations that NK efficacy is stronger than we indicate. We do not draw conclusions about the efficiency of NK cells from our model. Rather, we use the model equations as a possible description of the different cytolytic mechanisms of NK cells versus CD8 T cells. These mathematical descriptions of the immune cell dynamics are validated when we show that the simulations can reproduce experimentally observed differences in the efficacy of innate and the tumor-specific responses. An explicit statement of the initial conditions used was omitted in ref. 1, so we state them here. Figure 4 (right) of ref. 1 is a simulation that captures the behavior shown in Fig. 3D (right-most panel) of ref. 2. The simulation employed a parameter set using a modified scaling of NK parameters from Table 1 of ref. 1 and nonzero NK initial conditions. The same qualitative simulation outcomes can be obtained using the NK parameters in Table 1, with j(ln) = 6j(nn), and with the initial NK count at its steady-state value: NK0 = r/f = 3.16 10 cells. The initial CD8 T count is zero, and the initial tumor challenge is T0 = 10 4 cells, with a re-challenge on day 10 of 10 live cells. We note that any values for j are rough estimates because precise values were not to be found in the literature. We also point out that for the first 10 days of the simulation, the ‘‘ligand-transduced’’ parameter set for the NK cells was used, and from day 10 onward, the ‘‘control-transduced’’ parameter set was employed. This reflects the conditions of the laboratory experiment. We conjecture, based on their simulations, that Gowal et al. neglected to change the parameter set on day 10. We can only reproduce their results when the ligand-transduced parameter set is used for the entire simulation. This naturally results in a much stronger immune suppression of the tumor, but does not reflect the experiment reported in ref. 2. The image on Fig. 4 (bottom left) of ref. 1 represents the outcomes of the experiments of Fig. 2A of ref. 2. In this case, only CD8 T cells were targeted for deactivation. However, because of potential cross-reactions, including the loss of IL-2 production by the T cells, which in turn, could diminish NK differentiation and maturation, we assume that initial NK cell counts were lower than the steady state, but certainly not zero, as conjectured by Gowal and colleagues. Initial NK was NK0 = 10 4
No influence of ischemic preconditioning on running economy

Many of the potential performance-enhancing properties of ischemic preconditioning suggest that the oxygen cost for a given endurance exercise workload will be reduced, thereby improving the economy of locomotion. The aim of this study was to identify whether ischemic preconditioning improves exercise economy in recreational runners. A randomized sham-controlled crossover study was employed in which 18 adults (age 27 ± 7 years; BMI 24.6 ± 3 kg/m2) completed two, incremental submaximal (65–85% VO2max) treadmill running protocols (3 × 5 min stages from 7.2–14.5 km/h) coupled with indirect calorimetry to assess running economy following ischemic preconditioning (3 × 5 min bilateral upper thigh ischemia) and sham control. Running economy was expressed as mlO2/kg/km and as the energy in kilocalories required to cover 1 km of horizontal distance (kcal/kg/km). Ischemic preconditioning did not influence steady-state heart rate, oxygen consumption, minute ventilation, respiratory exchange ratio, energy expenditure, and blood lactate. Likewise, running economy was similar (P = 0.647) between the sham (from 201.6 ± 17.7 to 204.0 ± 16.1 mlO2/kg/km) and ischemic preconditioning trials (from 202.8 ± 16.2 to 203.1 ± 15.6 mlO2/kg/km). There was no influence (P = 0.21) of ischemic preconditioning on running economy expressed as the caloric unit cost (from 0.96 ± 0.12 to 1.01 ± 0.11 kcal/kg/km) compared with sham (from 1.00 ± 0.10 to 1.00 ± 0.08 kcal/kg/km). The properties of ischemic preconditioning thought to affect exercise performance at vigorous to severe exercise intensities, which generate more extensive physiological challenge, are ineffective at submaximal workloads and, therefore, do not change running economy.
Ten-year analysis of the prospective multicentre Chemo-N0 trial validates American Society of Clinical Oncology (ASCO)-recommended biomarkers uPA and PAI-1 for therapy decision making in node-negative breast cancer patients.

Final 10-year analysis of the prospective randomised Chemo-N0 trial is presented. Based on the Chemo-N0 interim results and an European Organisation for Research and Treatment of Cancer (EORTC) pooled analysis (n=8377), American Society of Clinical Oncology (ASCO) and Arbeitsgemeinschaft Gynäkologische Onkologie (AGO) guidelines recommend invasion and metastasis markers urokinase-type plasminogen activator (uPA)/plasminogen activator inhibitor-1 (PAI-1) for risk assessment and treatment decision in node-negative (N0) breast cancer (BC).



The final Chemo-N0 trial analysis (recruitment 1993-1998; n=647; 12 centres) comprises 113 (5-167) months of median follow-up. Patients with low-uPA and PAI-1 tumour tissue levels (n=283) were observed. External quality assurance guaranteed uPA/PAI-1 enzyme-linked immunosorbent assay (ELISA) standardisation. Of 364 high uPA and/or PAI-1 patients, 242 agreed to randomisation for CMF chemotherapy (n=117) versus observation (n=125).



Actuarial 10-year recurrence rate (without any adjuvant systemic therapy) for high-uPA/PAI-1 observation group patients (randomised and non-randomised) was 23.0%, in contrast to only 12.9% for low-uPA/PAI-1 patients (plog-rank=0.011). High-risk patients randomised to cyclophosphamide-methotrexate-5-fluorouracil (CMF) therapy had a 26.0% lower estimated probability of disease recurrence than those randomised for observation (intention-to-treat (ITT)-analysis: hazard ratio (HR) 0.74 (0.44-1.27); plog-rank=0.28). Per-protocol analysis demonstrated significant treatment benefit: HR 0.48 (0.26-0.88), p=0.019, disease-free survival (DFS) Cox regression, adjusted for tumour stage and grade.



Chemo-N0 is the first prospective biomarker-based therapy trial in early BC defining patients reaching good long-term DFS without adjuvant systemic therapy. Using a standardised uPA/PAI-1 ELISA, almost half of N0-patients could be spared chemotherapy, while high-risk patients benefit from adjuvant chemotherapy. These 10-year results validate the long-term prognostic impact of uPA/PAI-1 and the benefit from adjuvant chemotherapy in the high-uPA/PAI-1 group at highest level of evidence. They thus support the guideline-based routine use of uPA/PAI-1 for risk-adapted individualised therapy decisions in N0 breast cancer.
Lung function and disability in neuromuscular patients at first admission to a respiratory clinic.

Respiratory failure is the most common cause of morbidity and mortality in patients with neuromuscular diseases (NMD). Non-invasive mechanical ventilation is considered highly effective for treating chronic respiratory failure. Perception and knowledge of risks associated with respiratory derangements may be underestimated.



The aim of our study was to evaluate the association among respiratory function, general clinical disability and need of home mechanical ventilation (HMV) in patients with slowly progressive NMD admitted for the first time to dedicated respiratory outpatient clinics.



Anthropometrics, lung function, respiratory muscle function, daytime blood gases data, and general clinical disability assessed by means of a clinical interview were recorded. Indication for HMV was an arterial CO(2) tension >45mmHg and/or a vital capacity <50% predicted, and/or maximal inspiratory pressure <60cmH(2)O.



Two out of 5 patients complained of dyspnoea during daily activity and dysphagia, while more than 1/3 had ineffective cough and speech difficulties. Two-third of the whole group were considered to need HMV. By applying one or more criteria for NMD diagnosis, great variability was found for indication to HMV. Clinical disability was inversely related to dynamic and static lung volumes, and to respiratory muscle function.



About two-third of NMD patients admitted to a respiratory clinic is a candidate for home mechanical ventilation being their clinical derangement inversely related with respiratory function. The use of a simple dedicated clinical disability interview may reduce underestimation of HMV need.
Retrieval of immature oocytes after chemotherapy for Hodgkin's disease and prolonged ovarian down-regulation with gonadotropin-releasing hormone agonist.

To describe isolation and in vitro maturation of primary oocytes from the ovarian cortex in the presence of hypothalamic pituitary down-regulation.



Case report.



Tertiary care university-affiliated hospital.



An 18-year-old patient was given treatment with the ABVD (Adriamycin, bleomycin, vinblastine, and dacarbazine) protocol for Hodgkin's disease. She underwent ovarian tissue cryopreservation while being cotreated with GnRH agonist because of disease relapse.



Laparoscopic oophorectomy, ovarian tissue cryopreservation, and in vitro maturation of primary oocytes.



Maturation of primary oocytes isolated from the medium used for preparation of ovarian tissue.



Twenty-one immature germinal vesicle-stage oocytes were isolated from the medium of dissection. All were incubated in in vitro maturation medium, and five were maturated and frozen.


CONCLUSION(S)
The fact that germinal vesicle-stage oocytes were present in our patient's medium despite hormonal down-regulation demonstrates that GnRH agonist does not completely inhibit antral follicle development.
Early age-dependent growth impairment in chronic renal failure

We report early linear growth in 73 children (51 boys, 22 girls) with early onset of chronic renal failure (CRF). The inclusion criteria was onset of CRF before 6 months of age, two or more height measurements during the 1st year of life, follow-up for at least 3 years and continuously impaired renal function with a glomerular filtration rate below 50 ml/min per 1.73 m2 at 1 year or later. Only height measurements taken during conservative treatment or dialysis were included. The data were analysed in terms of the infancy-childhood-puberty growth model. There was an age-dependent growth failure in early life leading to an attained height of −3 standard deviation score (SDS) at 3 years of age. Approximately one-third of the reduction in height occurred during fetal life and one-third during the first postnatal months. Between 0.75 and 1.5 years of age height also decreased by 1 SD as a consequence of a delayed onset of the second, the “childhood’, phase of growth in 36% of the patients and by an ‘offset childhood’ growth pattern — i.e. a return to the infancy phase pattern after onset of the childhood phase — in 60% of the patients. Growth between 0.25–0.75 and 1.5–5 years of age was generally percentile parallel and thus less likely to be affected in CRF with early disease onset. The glomerular filtration rate was not related to the height gain in early life. We speculate that the growth failure during fetal life and the first postnatal months reflects metabolic and/or nutritional influences and the impaired growth at 0.75–1.5 years of age is related to a partial insensitivity to growth hormone.
Responses to dynamic head-and-body tilts are enhanced in Parkinson's disease.

Previous studies demonstrated that destabilizing responses to slow perturbations were enhanced in patients with Parkinson's disease (PD). Our objectives were to investigate the influence of PD on responses to faster whole head-and-body tilts in the standing position, and to establish whether any modification of tilt-evoked responses in PD patients was related to possible changes in the modulation of soleus (SO) H-reflex.



Ten PD patients and 10 age-matched normal subjects assumed a standing position on an L-shaped tilting apparatus. Their head and shoulders were firmly attached to the back support of the apparatus, while their feet were fixated to the standing platform. With their vision occluded, the subjects's whole head-and-body was suddenly tilted forward to 20 degrees, at a peak head acceleration of 0.7 g +/- 0.1 g. Tilt-evoked responses were recorded from the lower limb muscles bilaterally. In addition, 40 H-reflexes were elicited in the SO muscle at 30-190 ms intervals after the onset of head acceleration. The M response amplitude was kept within +/- 15% of its control value.



PD patients demonstrated an abnormally high responsiveness to whole head-and-body tilts in comparison with age-matched normal subjects. This was shown by the significantly larger proportion of PD patients manifesting responses in the SO, biceps femoris and vastus lateralis muscles (p < 0.05), as well as their significantly larger SO response area (413%; p < 0.01). In contrast, the amplitude of the SO H-reflex was significantly increased by only 14% (p < 0.05) in these patients, and only at 30-70 ms after head acceleration onset.



The overexcitable tilt-evoked responses of PD patients could originate from a reduced ability to suppress responses when the body is supported. This enhanced excitability of tilt-evoked responses was probably not due to motoneuronal hyperexcitability or decreased presynaptic inhibition of the group Ia terminals involved in the mainly monosynaptic H-reflex pathway. Thus, we hypothesize that the control of spinal interneurons involved in the tilt-evoked responses may be defective in PD.
Quality of life of individuals with stroke and their caregivers in a city of Triângulo Mineiro.

To compare the quality of life (QoL) of individuals with stroke and their caregivers.



This is an observational cross-sectional survey, involving 83 individuals who suffered a stroke. The participants were divided into four groups: group of individuals with stroke who have caregivers (44), group of individuals with stroke without caregivers (39), group of caregivers (44) and a reference group (83) in the period of March to May 2010. To assess QoL, the instrument used was the WHOQOL-bref.



The highest scores for the four fields were observed increasingly for the group of individuals with stroke with caregivers, the stroke group without caregivers followed by the group of caregivers and the reference group. The comparison of scores between groups showed that the presence of stroke and the fact of being caregiver affect QoL in all domains of WHOQOL-bref.



It was possible to understand the negative impact that stroke causes in the lives of the affected ones and their caregivers, in order to better target public health policies.
Quality of life of colorectal cancer patients in certified centers versus non-certified hospitals.

Since 2006, in Germany colorectal cancer patients can be treated in certified colorectal cancer centers. The aim of this explorative study was to investigate whether there are differences in the quality of life (QoL) of colorectal cancer patients who were treated in certified versus noncertified centers.



A total of 284 colorectal cancer patients participated in the study: 184 patients from certified colorectal cancer centers and 100 patients from noncertified centers. Data on QoL (using the Quality of Life Questionnaire of the European Organization for Research and Treatment of Cancer (EORTC-QLQ C30)), patient satisfaction, mental distress and sociodemographic data were assessed with a questionnaire in a written survey after the hospital stay. The moderating influence of patientrelated characteristics (e.g. age, sex, patient satisfaction, and psychological distress) and cancerrelated factors (Union internationale contre le cancer (UICC) stage) were tested.



On a descriptive level, patients from noncertified centers had a higher QoL in 5 subdimensions (higher physical and role functioning and less insomnia, appetite loss and financial difficulties). After adjustment, only 2 differences remained significant: physical functioning (p < 0.01) and role functioning (p = 0.02).



Structural improvements in the oncological care are not necessarily reflected in a better QoL of the patients treated in certified colorectal cancer centers. The findings are discussed in the context of the applied study design.
Functional MR imaging in patients with carotid artery stenosis before and after revascularization.

Significant extracranial stenosis of the ICA is a known risk factor for future stroke and it has been shown that revascularization reduces the risk of future stroke. We applied BOLD fMRI in patients with carotid artery stenosis before and after CEA. Our purpose was to determine whether fMRI is able to demonstrate impaired CVR and to identify patient parameters that are associated with postoperative changes of cerebral hemodynamics.



Nineteen consecutive patients with symptomatic (n = 13) and asymptomatic (n = 6) stenosis of the ICA were prospectively recruited (male/female ratio = 16:3; age, 69 ± 8,1 years). fMRI using a simple bilateral motor task was performed immediately before and after CEA.



Mean BOLD MSC was significantly increased postoperatively (MSC, 0.13 ± 0.66; P = 0.0002). Patients with a stenosis of <80% demonstrated an increase in MSC (MSC, 0.32 ± 0.59; P ≤ .0001). Patients with previous ischemic stroke showed a larger MSC than patients with TIAs (stroke: MSC, 0.55 ± 0.65; P ≤ .0001; TIA: MSC, 0.05 ± 0.26; P = 0.054). Patients older than 70 years had a significantly larger MSC following surgery (≤70 years: MSC, -0.01 ± 0.39; P = .429; >70 years: MSC, 0.29 ± 0.48; P ≤ .0001).



BOLD fMRI can demonstrate changes in cerebral hemodynamics before and after CEA, indicative of an ameliorated CVR. This response is dependent on the age of the patient, the degree of preoperative stenosis, and the patient's symptoms.
Prevalence of chronic kidney disease in a representative sample of the Polish population: results of the NATPOL 2011 survey.

Chronic kidney disease (CKD) has been proven to be a major risk factor of cardiovascular disease (CVD). Until now, data on the prevalence of CKD among adults in Poland were limited. The NATPOL 2011 survey is a cross-sectional observational study designed to assess the prevalence and control of CVD risk factors in Poland, and the first study capable of evaluating CKD prevalence in adult Polish citizens.



Serum creatinine concentration and the urine albumin-to-creatinine ratio (ACR) were measured in 2413 randomly selected participants (ages 18-79 years) from a national survey study. CKD was diagnosed if the estimated glomerular filtration rate (eGFR) was <60 mL/min/1.73 m(2) or ≥60 mL/min/1.73 m(2) with coexisting albuminuria (ACR ≥ 30 mg/g). Additionally, comorbidities and anthropometric and social factors related to the prevalence of CKD were analysed.



The prevalence of CKD was estimated at 5.8% [95% confidence interval (95% CI) 4.6-7.2] using Chronic Kidney Disease Epidemiology Collaboration formula. The general prevalence was higher when the MDRD was applied [6.2% (95% CI 4.0-7.6)]. An eGFR <60 mL/min/1.73 m(2) was found in 1.9% (95% CI 1.5-2.5) of the studied population. This was accompanied by low awareness of this condition (14.9%). The frequency of albuminuria was estimated at 4.5% (95% CI 3.4-5.9). Diabetes mellitus (DM) and arterial hypertension (AH) were more frequent among respondents with diagnosed CKD compared with those without CKD [18.5 versus 4.5% (P < 0.001) and 67.8 versus 29.0% (P < 0.001) respectively]. DM and AH were, apart from increasing age, the two greatest risk factors of CKD.



The estimated prevalence of CKD among adults in Poland is 5.8% (∼1 724 960 patients). Its prevalence was lower than expected. CKD is more frequent in older subjects, smokers and people with comorbidities such as AH and DM.
An Open-Label Prospective Randomized Multicenter Study Shows Very Rapid Remission of Ulcerative Colitis by Intensive Granulocyte and Monocyte Adsorptive Apheresis as Compared With Routine Weekly Treatment

Granulocyte and monocyte adsorptive apheresis (GMA) has shown efficacy in patients with active ulcerative colitis (UC). However, with routine weekly treatment, it may take several weeks to achieve remission, and to date, the efficacy of a more frequent treatment schedule remains unknown. The aim of this study was to assess the clinical efficacy and safety of intensive GMA treatment in patients with active UC.METHODS:This was an open-label, prospective, randomized multicenter study to compare an intensive, two GMA sessions per week, with the routine, one GMA session per week. A total of 163 patients with mild-to-moderately active UC were randomly assigned to routine weekly treatment or intensive treatment. The maximum number of sessions of GMA permitted was 10. However, when patients achieved remission, GMA was discontinued. Remission rate at the end of the study, time to remission, and adverse events were assessed in both groups.Of the 163 patients, 149 were available for efficacy analysis as per protocol, 76 were in weekly GMA, and 73 were in intensive GMA. At the end of the study period, clinical remission was achieved in 41 of 76 patients (54.0%) in weekly GMA and in 52 of 73 patients (71.2%) in intensive GMA (P=0.029). The mean time to remission was 28.1±16.9 days in the weekly GMA treatment group and 14.9±9.5 days in the intensive GMA group (P<0.0001). Intensive GMA was well tolerated without GMA-related serious adverse side effects.Intensive GMA in patients with active UC seems to be more efficacious than weekly treatment, and significantly reduced the patients' morbidity time without increasing the incidence of side effects.
Repetitive transcranial magnetic stimulation is as effective as electroconvulsive therapy in the treatment of nondelusional major depressive disorder: an open study

Repetitive transcranial magnetic stimulation (rTMS), a new method for the stimulation of the central nervous system, is being proposed as a potential new treatment in patients with major depressive disorder (MDD). We tested the hypothesis that rTMS would be as effective as electroconvulsive therapy (ECT) in patients with MDD.



Forty patients with MDD referred for ECT were randomly assigned to either ECT or rTMS. Repetitive transcranial magnetic stimulation was performed at 90% power of the motor threshold. The stimulation frequency was 10 Hz for either 2 sec (first eight patients) or 6 sec (final 12 patients) for 20 trains. Patients were treated for up to 20 treatment days. Electroconvulsive therapy was performed according to standard protocols.



Overall patients responded best to ECT (chi(2) = 3.8, p <.05). Patients with MDD and psychosis responded significantly better to ECT (chi(2) = 9.2, p <. 01), whereas MDD patients without psychosis responded similarly to both treatments (chi(2) = 0.0, ns). The analysis of variance with repeated measures of clinical variables for the whole sample revealed significant treatment effects for both groups; however, interaction between group and treatment was seen only for the Global Assessment of Function and the Sleep assessment. When the psychosis-nonpsychosis grouping was considered, patients with psychosis responded dramatically better to ECT in all assessments, whereas those without psychosis responded similarly to both treatments.



Overall ECT was a more potent treatment for patients with MDD, this being particularly evident in patients with MDD and psychosis; however, in patients with MDD without psychosis the effects of rTMS were similar to those of ECT. The results we report are encouraging and support an important role for rTMS in the treatment of severe MDD; however, additional blinded studies are needed to precisely define this role.