Physics-informed machine learning: case studies for weather and climate modelling

Machine learning (ML) provides novel and powerful ways of accurately and efficiently recognizing complex patterns, emulating nonlinear dynamics, and predicting the spatio-temporal evolution of weather and climate processes. Off-the-shelf ML models, however, do not necessarily obey the fundamental governing laws of physical systems, nor do they generalize well to scenarios on which they have not been trained. We survey systematic approaches to incorporating physics and domain knowledge into ML models and distill these approaches into broad categories. Through 10 case studies, we show how these approaches have been used successfully for emulating, downscaling, and forecasting weather and climate processes. The accomplishments of these studies include greater physical consistency, reduced training time, improved data efficiency, and better generalization. Finally, we synthesize the lessons learned and identify scientific, diagnostic, computational, and resource challenges for developing truly robust and reliable physics-informed ML models for weather and climate processes. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Agreement between heart rate deflection point and maximal lactate steady state in young adults with different body masses

We examined the agreement between heart rate deflection point (HRDP) variables with maximal lactate steady state (MLSS) in a sample of young males categorized to different body mass statuses using body mass index (BMI) cut-off points. One hundred and eighteen young males (19.9 ± 4.4 years) underwent a standard running incremental protocol with individualized speed increment between 0.3 and 1.0 km/h for HRDP determination. HRDP was determined using the modified Dmax method called S.Dmax. MLSS was determined using 2-5 series of constant-speed treadmill runs. Heart rate (HR) and blood lactate concentration (La) were measured in all tests. MLSS was defined as the maximal running speed yielding a La increase of less than 1 mmol/L during the last 20 min. Good agreement was observed between HRDP and MLSS for HR for all participants (±1.96; 95% CI = -11.5 to +9.2 b/min, ICC = 0.88; P < 0.001). Good agreement was observed between HRDP and MLSS for speed for all participants (±1.96; 95% CI = -0.40 to +0.42 km/h, ICC = 0.98; P < 0.001). The same findings were observed when participants were categorized in different body mass groups. In conclusion, HRDP can be used as a simple, non-invasive and time-efficient method to objectively determine submaximal aerobic performance in nonathletic young adult men with varying body mass status, according to the chosen standards for HRDP determination.

Uropathogenic Escherichia coli in the high vaginal swab samples of fertile and infertile women: virulence factors, O-serogroups, and phenotyping and genotyping characterization of antibiotic resistance

Transmission of urinary tract infections into the reproductive system is unavoidable. The present research was performed to assess the distribution of virulence genes, O-serogroups and antibiotic resistance properties of uropathogenic Escherichia coli (UPEC) strains isolated from the high vaginal swab samples of fertile and infertile women. A total of 460 high vaginal swab samples were taken from fertile and infertile women. Distribution of virulence factors and serogroups and antibiotic resistance properties of the E. coli isolates were assessed. Sixty-five out of 460 (14.13%) swab samples were positive for E. coli. Prevalences of E. coli in samples taken from fertile and infertile women were 13.63% and 14.58%, respectively. O1 (7.69%), O2 (6.15%) and O6 (6.15%) were the most frequently detected serogroups. The most frequently detected virulence genes were sfa (72.72%), afa (72.72%), cnf1 (72.72%) and fim (72.72%). The most commonly detected antibiotic-resistance genes were tetA (95.45%), CITM (88.63%), aac(3)-IV (86.36%) and sul1 (72.72%). UPEC strains harboured the highest prevalence of resistance against tetracycline (88.63%), ampicillin (79.54%), gentamicin (77.27%) and enrofloxacin (52.27%). Seventeen out of 26 (65.38%) UPEC strains isolated from infertile women were resistant toward more than ten antibiotic agents. Infertile women with a history of urinary tract infections had the higher prevalence of UPEC strains and also the other characters. High prevalence of the virulent and resistant UPEC strains in the high vaginal part of the infertile women with a history of urinary tract infections may show an important role of these pathogens as causes of female infertility. However, further research is required to confirm this hypothesis.

Effect of psychosocial care model applied in an "elderly day care center" on loneliness, depression, quality of life, and elderly attitude

BACKGROUND

The purpose of the study is to evaluate the effect of the model applied in order to meet psychosocial care needs of elderly people in an elderly day care center on loneliness, depression, quality of life, and elderly attitude.

METHOD

An intervention program prepared for the psychosocial needs of elderly people was carried out in the study and it was evaluated as pretest-posttest. The data were collected with UCLA Loneliness Scale (UCLA, LS), Geriatric Depression Scale Short Form (GDS-SF), Turkish version of the WHO Quality of Life Instrument Older Adults Module (WHOQOL-OLD-TR) and Turkish version of the WHO - Atittudes of Aging Questionnaire (AAQ-TR) in the study. The psychosocial intervention program was conducted once in a week, nine sessions were held in total and each of them took 90-120 min.

RESULTS

A statistically significant difference was found between the points that the elderly people obtained from the prior to and after UCLA Loneliness Scale and WHOQOL-OLD. TR instrument (P < 0.05). Besides, the difference between points gotten from the subdimensions "general," "psychosocial loss," and "psychosocial change" of AYTA-TR Scale was statistically significant.

CONCLUSION

The intervention provided for the psychosocial needs of elderly people led to positive results in loneliness perception, quality of life, and elderly attitudes. Therefore, it is thought that this model is appropriate to be used commonly by nurses in psychosocial care of elderly people.

Molecular Detection of Chlamydia felis in Cats in Ahvaz, Iran

Chlamydiae are obligate generally Gram-negative intracellular parasites with bacterial characteristics, including a cell wall, DNA, and RNA. They have a worldwide distribution in different animal species. Chlamydia felis (C. felis) is an important agent with zoonotic susceptibility often isolated from cats with chronic conjunctivitis. The aim of the present survey aimed to determine the molecular occurrence of C. felis in cats in Ahvaz, Iran. In this regard, a total of 152 cats (126 households and 26 feral) were included in the current study. After recording their history information, two swabs were taken from the oropharyngeal cavity and eye conjunctiva of the investigated cats. The extraction of DNA was followed by PCR targeting the pmp gene of C. Felis. In the next step, the positive samples were sequenced based on the Gene Bank. Out of 152 samples, 35 (23.03%) were positive using polymerase chain reaction technique (95% CI: 16.30-29.70). Regarding infection with Chlamydiosis, the obtained results showed a significant difference between cats suffering from ocular or respiratory diseases (44.64%; 25 out of 56) and the healthy ones (10.42%; 10 out of 96; P=0.01). The prevalence of infection was significantly higher in cats younger than 1 year (34.12%; 29 out of 85), compared to those older than 1 year (8.96%; 6 out of 67; P=0.02). No significant difference was noted in terms of gender (25.45% in males and 21.65% in females), breed (23.81% in DSH and 19.23% in Persian), and lifestyle (22.22% companions [28 out of 126] and 26.92% ferals [7 out of 26]; P&amp;gt;0.05). It can be concluded that a significant number of cats are infected with C. felis in Ahvaz. The use of molecular tests, such as PCR, has revolutionized the diagnosis of chlamydial infections.

Occurrence of purulent mandibular and maxillary osteomyelitis associated with Pseudomonas aeruginosa in a sheep flock in south-west of Iran

This report describes an outbreak of purulent mandibular and/or maxillary osteomyelitis caused by Pseudomonas aeruginosa in a sheep flock located in the Khuzestan province, Iran. Jaw bones of almost 100 out of 500 mature sheep in a flock became severely deformed with a variably sized firm swelling, without any signs of inflammation in the surrounding soft tissues. The affected animals showed anorexia, depression, swelling of the mandibular and/or maxillary area, loss of cheek teeth and poor body condition. ‏These animals were gradually culled in a period of 3 months. Postmortem examination showed a hard swelling of jaw bones with dirty greenish pus that filled alveolar molar teeth cavities. Histopathologic findings revealed necrotic areas surrounded by mixed population of inflammatory cells with exuberant fibrosis around some area of the lesions and irregular trabeculae of woven bone. In bacteriology, pure culture of P. aeruginosa was isolated from all of 7 sampled sheep. Based on clinical examination, radiography, histopathological features and bacteriology, the lesions were diagnosed as chronic suppurative osteomyelitis caused by P. aeruginosa. According to bacteriological results, the likely source of bacterial infection in this study was drinking water.

Do the types of treatments after hysteroscopic resection of septate uterus cause different results?

BACKGROUND

Two protocols are generally performed after the following hysteroscopic resection of septate uterus to prevent Asherman's syndrome in Iran. The aim of this study was to assess and compare the postoperative complication rate by alternate and constant therapy following hysteroscopic septum resection procedure.

MATERIALS AND METHODS

The authors conducted a retrospective interventional study on secondary data obtained from the medical records of 106 infertile women with septate uterus who underwent a hysteroscopic resection between April 2005 and February 2014. After septum resection, 71 patients received alternate hormonal therapy and 35 patients received constant hormonal therapy. All the women were followed-up postoperatively with interview and physical examination for more than six months.

RESULTS

Of the 71 women who received alternate hormonal therapy, 16 (22.5%) had spotting. While in the constant protocol therapy group, the rate of the spotting during the follow-up period was reported in 13 (37.1%) patients. There was no significant difference between the two groups in terms of spotting complication after the septum resection. Self-reported breast tenderness as complications of hormonal therapy after septum resection in constant protocol was greater than in alternate protocol group (21.1% vs. 60.0%) (p < 0.0001).

CONCLUSION

The result of this study indicated that hormonal therapy complications following hysteroscopic resection of septate uterus in both protocols was the same.

Testicular lesions and epididymal sperm parameters in the Iranian river buffalo (Bubalus bubalis)

The aim of this study was to evaluate the testicular lesions and their effects on the epididymal sperm parameters in the Iranian river buffalo (Bubalus bubalis). Total numbers of 117 scrota from the pubertal buffalo were provided from the local slaughterhouse. The samples were evaluated for morphological parameters and any macro- or microscopic lesions. The sterile swabs from the testis parenchyma were subjected to microbiology culture. The epididymal spermatozoon was analysed for concentration, progressive motility and abnormalities. The results showed 34.2% fibrotic adhesions between parietal and visceral layers of tunica vaginalis that was significantly different among seasons (P < 0.05). The cases of unilateral cryptorchidism and bilateral Sertoli cell tumour were detected, with no spermatozoa in the respected epididymides. Microscopic examination showed 13.25% (31/234) lesions including general (51.61%; 16/31) and multifocal (29.03%; 9/31) degenerations as well as interstitial orchitis (9.68%; 3/31) and the Sertoli cell tumour (6.45%; 2/31). No relationship between the lesions and the bacterial isolation (n = 6) was detected. The sperm parameters and morphological parameters of the testis were under influence of microscopic lesions (P < 0.05). In conclusion, the testicular macro- and microscopic lesions may have a noticeable contribution in the Iranian buffalo fertility.

Histopathologic and Radiographic evaluation of the electroacupuncture effects on ulna fracture healing in dogs

Acupuncture can affect bone healing by stimulation of sensory nerves and releasing of local and systemic neuropeptides. The purpose of this experimental study was to evaluate the effects of electroacupuncture on ulna fracture healing in dogs. In this study, 12 healthy dogs were randomly divided in to four equal groups, where group 1 was kept as control group and evaluated for 45 days, group 2: treatment group and evaluated for 45 days, group3: control group of 90 days and group 4: treatment group of 90 days. After induction of anesthesia, the ulna was cut with Gigli wire saw in each groups, 10 days after operation, the treatment (acupuncture) group was treated with 10 minutes electroacupuncture stimulations on the acupoints Kid1, Kid3, Kid6 and Kid7, for 10 days. Histopathologic samples of all dogs were harvested from bone osteotomized site in 45 and 90 days after surgery. Indices like, count of inflammatory cells, cartilaginous tissue, fibrotic tissue and deposition of collagen were evaluated on samples and classified with 0, 1, 2, and 3 degrees. Also, radiographic evaluation of the patients was applied using radiographic scoring system on days: 7, 15, 30, 45, 60 and 90 after surgery. This study revealed that, acupuncture had no effect on bone healing (p>0.05). Cause of non-significant difference changes between the control and treatment groups, and lack of complete healing in both groups may be due to lack of ulna bone fixation. Alternatively, selection of other acupoints in acupuncture could have a better healing role.

Histopathologic and Radiographic evaluation of the electroacupuncture effects on ulna fracture healing in dogs

Acupuncture can affect bone healing by stimulation of sensory nerves and releasing of local and systemic neuropeptides. The purpose of this experimental study was to evaluate the effects of electroacupuncture on ulna fracture healing in dogs. In this study, 12 healthy dogs were randomly divided in to four equal groups, where group 1 was kept as control group and evaluated for 45 days, group 2: treatment group and evaluated for 45 days, group3: control group of 90 days and group 4: treatment group of 90 days. After induction of anesthesia, the ulna was cut with Gigli wire saw in each groups, 10 days after operation, the treatment (acupuncture) group was treated with 10 minutes electroacupuncture stimulations on the acupoints Kid1, Kid3, Kid6 and Kid7, for 10 days. Histopathologic samples of all dogs were harvested from bone osteotomized site in 45 and 90 days after surgery. Indices like, count of inflammatory cells, cartilaginous tissue, fibrotic tissue and deposition of collagen were evaluated on samples and classified with 0, 1, 2, and 3 degrees. Also, radiographic evaluation of the patients was applied using radiographic scoring system on days: 7, 15, 30, 45, 60 and 90 after surgery. This study revealed that, acupuncture had no effect on bone healing (p>0.05). Cause of non-significant difference changes between the control and treatment groups, and lack of complete healing in both groups may be due to lack of ulna bone fixation. Alternatively, selection of other acupoints in acupuncture could have a better healing role.

Cardiorespiratory fitness, activity level, health-related anthropometric variables, sedentary behaviour and socioeconomic status in a sample of Iranian 7-11 year old boys

The purpose of this study was to evaluate cardiorespiratory fitness (CRF), activity level, some health-related anthropometric variables, sedentary behaviour and socioeconomic status (SES) of 7-11 year old boys in the city of Ardabil, Iran. Of 21 253 school boys aged 7-11 years, 766 participated in this study using the cluster sampling method. Subjects underwent standard anthropometry. One-mile test was used to evaluate V.O₂ max. BMI cut-off points were used to identify weight status. Child's TV watching and video playing daily time (TVVPT) was taken for sedentary behaviour evaluation. SES and activity level were measured by standard questionnaires. Of all participants, 8.9% (N=68) of students had CRF lower than normal and 58.6% (N=449) of them had inadequate physical activity. There was a significant adverse relationship between V.O₂ max and body mass index (BMI), waist to height ratio (WHtR), waist circumference (WC), and fat mass (FM) (p<0.05). A significant direct association between SES and both FM and TVVPT was observed (p<0.05). Significantly lower physical activity and V.O₂ max, and higher TVVPT were observed in the obese boys than their counterparts (p<0.05). The results of this study indicated a significant relationship between CRF and physical activity, and health-related anthropometric variables in a selected sample of 7-11 year boys. Moreover, the obese subjects had not only lower physical activity but also longer sedentary behaviour time than their counterparts.

Regulatory effect of caffeic acid phenethyl ester on type I collagen and interferon-gamma in bleomycin-induced pulmonary fibrosis in rat

Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown etiology. Recent investigations have demonstrated that the impaired immune response is a common characteristic feature of IPF. Unfortunately, no definitive and effective drug treatment is available that could improve or at least inhibit the progressive course of this fatal disease. That is why one of the main priorities of pulmonary fibrosis investigations is to identify novel and effective molecular targets for preventive and therapeutic interventions. caffeic acid phenethyl ester (CAPE) is one of the most interesting bioactive compounds extracted from bee propolis. It has been shown that CAPE has an antioxidant activity and modulatory impact on immune system. Accordingly, the aim of the present study was to investigate the regulatory effects of CAPE on the levels of type I collagen (COL-1) and Interferon-gamma (IFN-γ) in bleomycin (BLM)-induced pulmonary fibrosis. Immunohistochemistry procedure was employed to assess the effects of CAPE on lung tissue. In this study, male Sprague-Dawley rats were divided into 5 groups (n=8) included 1: Positive control group: bleomycin (BLM). 2: Negative (saline) control group. 3, 4: Treatment groups of 1 and 2: BLM+CAPE (5 and 10 μmol/kg/day, respectively). (5: Sham group: CAPE (10 μmol/kg/day). BLM application resulted in significant changes in the level of studied parameters as compared to the controls. CAPE could decrease type I collagen concentration, modulate IFN-γ level, increase the animals' body weight and decrease the lung index dose-dependently, compared with model group. In conclusion, CAPE may provide a novel therapeutic target for treating pulmonary fibrosis.